From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Jun 04 2013 - 08:46:07 CDT
James,
You could use VegaZZ (for free at http://www.ddl.unimi.it/) as GUI for
all listed. There you have graphical interface and some operations could
be done in, let say, semi-authomatic way. But, _it is strongly
recommendable to more carefully look on NAMD tutorials_.
PBC vectors are written in NAMD configuration file, not together with
coordinates. And for constraints you should make separate PDB file in
which may use occupancy or isotermal factor columns to assign
constrained atoms. For reference you should use same PDB that you use
for coordinates at the beginning of simulation (i.e. starting PDB of
equilibrated system ready for production run).
Branko
On 6/4/2013 3:25 PM, James Starlight 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, its 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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