From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Sep 13 2013 - 12:19:52 CDT
I don't know the answer to this question because I never used psfgen, but
I just want to warn you that, *if* what you're trying to accomplish is
having a neutral simulation system, *then* changing the protonation states
of titratable residues is the wrong way to do it. Valid reasons to change
the protonation states of titratable residues are:
- to set them to their most likely state given their pKa and chemical
environment
- to try a few different options if the above doesn't yield a clear-cut answer
For instance, it is not unusual for weak acid groups to become neutral in
a highly negative local environment (and your membrane seems to fit that
bill), so if that's why you're doing this, then it sounds reasonable.
On 09/13/2013 09:41 AM, James Starlight wrote:
> Dear Namd users!
>
> I have extra question about psfgen.
>
> In particular I'd like to set pronation states of the titrable residues of
> my protein (e.g neutralize side chains of some asp and glu (which names
> should be glup and aspp in the charm naming scheme). What commands should
> I add to my psfgen script for such purpose?
>
> James
>
>
> 2013/6/10 Norman Geist <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>>
>
> Hi James,____
>
> __ __
>
> you know that you can set the box dimensions before solvating?
> Additionally, you may not set a PBC box smaller, than the atoms are
> already placed, because the simulation will crash due the atom being
> initially wrapped into each other. Furthermore, as it is a PBC box, it
> doesn’t matter if your box is centered or not. Think about it.____
>
> __ __
>
> Norman Geist.____
>
> __ __
>
> *Von:*owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>]
> *Im Auftrag von *James Starlight
>
>
> *Gesendet:* Freitag, 7. Juni 2013 07:14
> *An:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> *Betreff:* Re: namd-l: First meeting with NAMD____
>
> __ __
>
> One extra question-
>
> definition of the PBC vectors
>
> assuming that I have system protein in water, visualization in VMD
> give me the next min max and initial center coordinates of my solvated
> system
>
> vmd > measure minmax $everyone
> {2.0339999198913574 44.51599884033203 -6.256999969482422}
> {62.07699966430664 116.66600036621094 62.32600021362305}
> vmd > measure center $everyone
> 32.14433288574219 80.72885131835938 27.922433853149414
> vmd >
>
>
>
> than I've defining rectangular box with vectors
>
> cellBasisVector1 60.0 0.0 0.0
> cellBasisVector2 0.0 60.0 0.0
> cellBasisVector3 0.0 0.0 60.0
> cellOrigin 30.0 30.0 30.0
>
> In that case I dont need big value on Y (possible max up to 116 ). AS
> the result If I vary cell origin in Y from 0 to 60 my system will
> placed outside of PBC. With center on the y = 30 protein placed on
> bottom of the box. But how I can place in the middle of box on y
> dimension (I have no problem with X and Z in the same box) fixed y up
> to 60 ? (If I increade it up to maximun my protein will be placed
> correctly but I've obtain very big box.
>
>
> James____
>
> 2013/6/6 Norman Geist <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>>____
>
> Hi James,____
>
> ____
>
> Do you mean you did the whole equilibration while restraining
> positions of all atoms of the protein? If so, please think about what
> a minimization and equilibration is meant for. The error you see
> means, that in the moment where the restrains are removed, high forces
> were unloading which blows apart you system. This is of course due not
> allowing the protein to remove these tensions while the minimization
> and equilibration steps. You should at least free the protein during
> minimization. If you need to restrain anything, try to do it relative
> here not absolute (position), check out the “extrabonds” command.____
>
> ____
>
> If I got you wrong, please explain more detailed what exactly you did.____
>
> ____
>
> Norman Geist.____
>
> ____
>
> *Von:*owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>]
> *Im Auftrag von *James Starlight____
>
>
> *Gesendet:* Mittwoch, 5. Juni 2013 12:22
> *An:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>____
>
> *Betreff:* Re: namd-l: First meeting with NAMD____
>
> ____
>
> Today I've tried to perform small simulation of the water-soluble
> protein (gfp with embedded chromophore).
>
> After minimisation + nvt+ nvp equilibration with applied position
> restraines to all protein atom my simulation was crushed during
> begining of the production run with the eror
>
> LDB: =============== DONE WITH MIGRATION ================ 57.1231
> Info: Benchmark time: 4 CPUs 0.055768 s/step 0.322732 days/ns 108.641
> MB memory
> ERROR: Constraint failure in RATTLE algorithm for atom 938!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> ====================================================
>
> WallClock: 57.500668 CPUTime: 57.500668 Memory: 108.890625 MB
> Program finished.
>
> According to the error 938 atom correspond to the N-term of the
> residue connected to the chromophore of my GFP which I've included to
> the rest of backbone by means of psfgen.
>
> Also I've observed behavior of my system during minimisation and
> equilibration and didnt observe any significant artifacts (the
> geometry of the chromophore and connected to it residues was correct).
>
> Below you can see my parameters of simulation.
>
>
>
> structure ionized.psf
> coordinates ionized.pdb
> outputName md
> bincoordinates npt.restart.coor
> binvelocities npt.restart.vel
> extendedSystem npt.restart.xsc
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> parameters FP.prm
>
>
>
> cellBasisVector1 62.0 0. 0.0
> cellBasisVector2 0.0 80.0 0.0
> cellBasisVector3 0.0 0 62.0
> cellOrigin 31.0 40.0 31.0
>
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 2 ;# damping coefficient (gamma) of 5/ps
> langevinTemp 310
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.0
> langevinPistonDecay 500.0
> langevinPistonTemp 310
>
> Does it contain any errors assuming that I'm simulating water soluble
> protein in NPT conditions?
>
>
> 2) Could you provide me with the example of the input file for psfgen
> for automate hydrogen addition according to the existing protonation
> state ? I've tried to save my structure from VMD (according to the
> tutorial) but the hydrogens havent been added in that case
>
> Thanks for any suggestions,
>
> James____
>
> 2013/6/4 Giacomo Fiorin <giacomo.fiorin_at_gmail.com
> <mailto:giacomo.fiorin_at_gmail.com>>____
>
> also I found that conf file should lack for barostat parameters (
> simulation in NVT with weak coupling), shouldn't it ? Where I can
> read about NAMD equilibration protocols?____
>
> ____
>
> The NAMD manual!____
>
> ____
>
> 2) I have some problems with atom names (primarily with names of
> hydrogens) when I use charm36 (no problems with charm27) assuming
> that I add hydrogens by means of pdb2pqr where protonation state
> assigned with the charmm force field____
>
> ____
>
> Use psfgen to add the hydrogens again.____
>
> ____
>
>
>
> James____
>
> ____
>
> 2013/6/4 Giacomo Fiorin <giacomo.fiorin_at_gmail.com
> <mailto:giacomo.fiorin_at_gmail.com>>____
>
> Hello James, atom selections in VMD are your best friend here.
> First create a selection (VMD documentation is awesome for this)
> then:____
>
> ____
>
> 1) use the measure minmax command____
>
> 2) set the PDB occupancy for each atom to the force constant ____
>
> ____
>
> About the force field: why do you assume that charmm36, just
> because it's newer, doesn't contain the previous charmm27
> parameters?____
>
> ____
>
> G.____
>
> ____
>
> On Tue, Jun 4, 2013 at 10:33 AM, James Starlight
> <jmsstarlight_at_gmail.com <mailto:jmsstarlight_at_gmail.com>> wrote:____
>
> Dear colleagues!
>
> I've examined carefully basic NAMD tutorial (simulation of
> ubiquiteen) and briefly examined more advanced tutorials.
> Unfortunately I could not find answers on the questions
>
> 1) How quickly PBC vectors could be defined based on the
> dimensions of my system? (e.g I can define on each vector manually
> in VMD and show it by means of pbc box but I'm looking in more
> quick way to define box dimensions automatically and then add it
> to the conf file).
>
> 2) Is there any automatic tools for generation of the position
> restraints on the specific column in the pdb file ?
> I'll be thankful if you show me tutorial where both of that
> aspects as well as basic of the equilibration in namd was described.
>
> also I'm looking for the charm27 (prm and imp files) parameters
> with CMAP correcrions where parameters for lipids protein and
> waters-ions have been present. On the MacKerel webpage I found
> only newest charm36 params
>
> James____
>
> __ __
>
> 2013/6/4 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com
> <mailto:ajasja.ljubetic_at_gmail.com>>____
>
> Did you go through all the wonderful tutorials on NAMD
> <http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html>? The
> answers to both questions are there.____
>
> ____
>
> ____
>
> On 4 June 2013 15:25, James Starlight <jmsstarlight_at_gmail.com
> <mailto:jmsstarlight_at_gmail.com>> wrote:____
>
> Also some methodological questions
>
> 1- How I could properly define PBC vectors based on the input pdb
> ? ( for comparison gromacs gro format contain box vectors on the
> last string of the structure file ) Is there some VMD plugin to
> define pbc automatically ?
>
> 2- Defining constraints on the conf file
>
> #constraints
> constraints on
> consref ???
> conskfile ???
> conskcol X
>
> its important to define atoms on which that constraints will be
> included (??? in the above script where it correspond to the only
> protein atom) How it could be done?____
>
>
>
> James____
>
> 2013/6/4 James Starlight <jmsstarlight_at_gmail.com
> <mailto:jmsstarlight_at_gmail.com>>____
>
> Hi Norman!
>
> Thanks for suggestions again. Could you also help with the psfgen
> (Above I've described my problem)
>
> Here script that I used
>
> package require psfgen
> resetpsf
> topology top_crq_final.inp____
>
>
> topology top_all36_prot.rtf
> pdbalias residue HIS HSE
> segment A {____
>
> pdb prot_charm1.pdb
> first Nter
> last NONE
> }
> coordpdb prot_charm1.pdb A
>
> segment B {
> first NONE
> last Cter
> pdb prot_charm2.pdb
>
> }
> coordpdb prot_charm2.pdb B
>
>
> segment C {
> pdb crq.pdb
> first NONE
> last NONE
> }
> coordpdb crq.pdb C
>
> guesscoord
> patch link A:64 C:65
> patch link C:65 B:69
>
> writepsf dhp-output.psf
> writepdb dhp-output.pdb
>
> Here link correspond to the imaginary connection which I've found
> in the charm36 params
>
> PRES LINK 0.00 ! linkage for IMAGES or for joining segments
> ! 1 refers to previous (N terminal)
> ! 2 refers to next (C terminal)
> ! use in a patch statement
> ! follow with AUTOgenerate ANGLes DIHEdrals command
> BOND 1C 2N
> !the need for the explicit specification of angles and dihedrals in
> !patches linking images has not been tested
> !ANGLE 1C 2N 2CA 1CA 1C 2N
> !ANGLE 1O 1C 2N 1C 2N 2HN
> !DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
> !DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
> !DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
> !DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
> IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
> IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
>
>
> This produces reasonable geometry of chromophore embedded into the
> rest of the GFP barell but As I understood from the description I
> should provide some extra parameters for dihedrals and impropers
> for that connector regions. Assuming that chromophore is the part
> of the rest of backbone and standart parameters could be used from
> the backbone aminoacids how I could specifi it for that case ?
>
>
> Thanks for help,
>
> James____
>
> 2013/6/4 James Starlight <jmsstarlight_at_gmail.com
> <mailto:jmsstarlight_at_gmail.com>>____
>
> Hi Norman!
>
> Thanks for suggestions again. Could you also help with the psfgen
> (Above I've described my problem)
>
> Here script that I used
>
> package require psfgen
> resetpsf
> topology top_crq_final.inp____
>
>
> topology top_all36_prot.rtf
> pdbalias residue HIS HSE
> segment A {____
>
> pdb prot_charm1.pdb
> first Nter
> last NONE
> }
> coordpdb prot_charm1.pdb A
>
> segment B {
> first NONE
> last Cter
> pdb prot_charm2.pdb
>
> }
> coordpdb prot_charm2.pdb B
>
>
> segment C {
> pdb crq.pdb
> first NONE
> last NONE
> }
> coordpdb crq.pdb C
>
> guesscoord
> patch link A:64 C:65
> patch link C:65 B:69
>
> writepsf dhp-output.psf
> writepdb dhp-output.pdb
>
> Here link correspond to the imaginary connection which I've found
> in the charm36 params
>
> PRES LINK 0.00 ! linkage for IMAGES or for joining segments
> ! 1 refers to previous (N terminal)
> ! 2 refers to next (C terminal)
> ! use in a patch statement
> ! follow with AUTOgenerate ANGLes DIHEdrals command
> BOND 1C 2N
> !the need for the explicit specification of angles and dihedrals in
> !patches linking images has not been tested
> !ANGLE 1C 2N 2CA 1CA 1C 2N
> !ANGLE 1O 1C 2N 1C 2N 2HN
> !DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
> !DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
> !DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
> !DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
> IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
> IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
> IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
>
>
> This produces reasonable geometry of chromophore embedded into the
> rest of the GFP barell but As I understood from the description I
> should provide some extra parameters for dihedrals and impropers
> for that connector regions. Assuming that chromophore is the part
> of the rest of backbone and standart parameters could be used from
> the backbone aminoacids how I could specifi it for that case ?
>
>
> Thanks for help,
>
> James____
>
> ____
>
> 2013/6/4 Norman Geist <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>>____
>
> *Von:*owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> [mailto:owner-namd-l_at_ks.uiuc.edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>] *Im Auftrag von *James Starlight
> *Gesendet:* Montag, 3. Juni 2013 16:09
> *An:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> *Betreff:* namd-l: First meeting with NAMD____
>
> ____
>
> Dear NAMD users!
>
> Hi james,____
>
> ____
>
> ____
>
> Recently I've tried to launch my first simulation on NAMD :)
> (previously I've used Gromacs ). ____
>
> My questions:
>
>
> 1) Typical gromacs simulation consist of energy minimization +
> equilibration in NPT ensemble (with position restraints applied on
> each atoms of protein) + production run.
>
> As I understood minimization should explicitly defined in the conf
> file
>
> # Minimization
> minimize 100
> reinitvels $temperature
>
> run 5000000
>
> but what about equilibration stage ? ____
>
> How I can perform short simulation with the applied porses prior
> to the production run?____
>
>
> We usually have the following simulation protocol:____
>
> 1.Minimization for some thousand steps, depending on system size
> (check if TOTAL energy converges)____
>
> 2.Heating up using Langevin thermostat (there are multiple methods
> and thermostats available)____
>
> 3.Constant Pressure (remove vacuum bubbles from solvent using
> piston barostat, also other choices available)____
>
> 4.Heat again as pressure could have changed anything____
>
> 5.Free simulation <- production run____
>
> Each of these steps is represented by a own namd script.
> Additionally, each step uses the final coordinates and velocities
> from the step before, except minimization which start from the
> initial structure of course.____
>
> ____
>
> 2) How I can monitor total performance of the GPU utilized in the
> simulation assuming that I use CUDA.____
>
> ____
>
> Depending on what kind of GPU you got, you can try nvidia-smi to
> check for the utilization (I guess only for Tesla). But as others
> already said, you should use the CPU:GPU ratio and configuration,
> that comes with the smallest time/step. Additionally, for most
> system sizes I got a nice almost two-fold speedup by using
> “twoawayx yes” in my namd script, you should try the difference.
> To be sure to get the best performance, it’s worth it to do some
> benchmarks.____
>
> ____
>
>
> 3) I have parameters ( prm and inp files) for some non-standard
> residue ( GFP chromophore). for this protein I'd like to make
> model (including protein covalently bonded to the chromophore and
> solvent) and perform simulation. ____
>
> Could you provide me with the example or short tutorial for such
> task?____
>
>
> See VMD and psfgen. Additionally search for the NAMD Tutorial on
> the net, which is a really nice for starting for both NAMD and
> VMD.____
>
>
> Thanks for help,
>
>
> James____
>
> ____
>
> ____
>
> ____
>
> ____
>
> ____
>
> ____
>
> ____
>
> ____
>
> ____
>
> ____
>
> __ __
>
>
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