Re: First meeting with NAMD

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jun 04 2013 - 08:45:44 CDT

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, 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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