[gmx-users] MD after equilibration phase
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 6 16:37:30 CEST 2012
bipin singh wrote:
> Thanks for your comments.
> One more question.
> Does Gromacs saves velocities in pdb files, when we use gen_vel=yes
> option in mdp and save the output(-c) of mdrun as pdb file instead of
> gro file.
>
No. Velocities are only saved in the .trr and/or .cpt files. There is no place
for velocities in .pdb files.
-Justin
> On Fri, Apr 6, 2012 at 19:48, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 7/04/2012 12:15 AM, bipin singh wrote:
>> When we mention
>> gen_vel=no ;And provide pdb as input with no velocities
>>
>> As mentioned in the manual:
>> "The velocities are set to zero when there are no velocities in
>> the input structure file"
>>
>> Please elaborate what does this sentence mean.
>
> Each atom must have a velocity in a *dynamical* simulation. If there
> is no instruction for what values to use (i.e. not generated or
> supplied), zero is used. Integration proceeds from there, and this
> may or may not be stable, and certainly will not have the desired
> temperature (yet)...
>
> Mark
>
>
>>
>> On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> bipin singh wrote:
>>
>> Also, if we give continuation=yes in mdp file and use
>> input as pdb file as input instead of gro file, grompp
>> never complains....I don't no how it reads velocities from
>> pdb file (as no velocities are present in pdb files).
>> Ideally it should complain that no velocities found in
>> input file....
>>
>>
>> Again, the "continuation" keyword has nothing to do with
>> velocities. If you have "gen_vel = no" and you provide a .pdb
>> file with no velocities, then you do not preserve velocity
>> information. Whatever the initial forces are govern the
>> resulting motions. In any case, you do not preserve the
>> previous simulation conditions.
>>
>> -Justin
>>
>> On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <pcl at uab.edu
>> <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>>> wrote:
>>
>> On 2012-04-06 11:05:51AM +0400, James Starlight wrote:
>> > Dear Gromacs users!
>> >
>> >
>> > I have small question about order of the runs and
>> input data.
>> >
>> > Ussually I do 2 equilibration phases and subsequent
>> productive
>> phase in the
>> > conditions wich are equal to the last equilibration
>> phase ( e.g
>> often this
>> > is npt ).
>> >
>> > In the second equil.mdp and md.mdp there is option
>> >
>> > continuation = yes
>> >
>> > which means that there have been previous phases of the
>> simulation from
>> > wich coordinates and velocities should be taken.
>> >
>> > As I understood the coordinates is taken from .gro
>> file but from
>> what file
>> > the velocities must be providen ? Does it .cpt
>> checkpoint file from
>> > previous run? In some cases I've forgotten to define
>> -t npt.cpt
>> for my MD
>> > run providing only coordinates in GRO file, topology
>> and md.mdp
>> but I have
>> > not seen any errors in such simulation due to
>> absence of that
>> .cpt and
>> > GROMPP never remind me of the absense of this file.
>> What exactly
>> is in that
>> > .cpt file and from wich source the velocities from
>> equilibration
>> phase are
>> > taken ?
>>
>> continuation = yes is telling LINCS that it is a
>> continuation and
>> it should not attempt to refit the constrained bonds on
>> the first pass.
>>
>> The coords, velocities, state, and box information are
>> taken either
>> from the
>> cpt file or you can specify the previous .trr and it
>> will take the
>> last frame
>> from that and use it. If you used the output gro file
>> without -t, then
>> it will take coordinates and velocities from the .gro
>> but the
>> problem there
>> is the limited precision (3 decimal points for each).
>>
>> --
>>
>> ==================================================================
>> Peter C. Lai | University of
>> Alabama-Birmingham
>> Programmer/Analyst | KAUL 752A
>> Genetics, Div. of Research | 705 South 20th Street
>> pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>> | Birmingham AL
>>
>> 35294-4461
>> (205) 690-0808 |
>>
>> ==================================================================
>>
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>> --
>> -----------------------
>> /Regards,/
>> Bipin Singh
>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
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>> --
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>> /Regards,/
>> Bipin Singh
>>
>>
>>
>
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> /Regards,/
> Bipin Singh
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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