From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 04 2013 - 10:05:52 CDT
>
> 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****
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:15 CST