From: James Starlight (jmsstarlight_at_gmail.com)
Date: Fri Jun 07 2013 - 00:13:55 CDT
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>
> 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] *Im
> Auftrag von *James Starlight
>
> *Gesendet:* Mittwoch, 5. Juni 2013 12:22
> *An:* 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>****
>
> 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>****
>
> 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>
> 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>****
>
> 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> 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>****
>
> 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>****
>
> 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>****
>
> *Von:* 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
> *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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