From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 04 2013 - 09:38:15 CDT
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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