From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Jun 04 2013 - 09:46:54 CDT
Hello Giacomo,
thanks for suggestions!
in my conf file I've found two options for constrainded runs
consref < I think that its the pdb with the marked restrained
atoms
conskfile < I dont understand what is it :)
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?
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
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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