[gmx-users] MD after equilibration phase
bipin singh
bipinelmat at gmail.com
Fri Apr 6 16:36:14 CEST 2012
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.
On Fri, Apr 6, 2012 at 19:48, Mark Abraham <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> 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>> 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> | 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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>> ========================================
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>
>
>
> --
> -----------------------
> *Regards,*
> Bipin Singh
>
>
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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--
-----------------------
*Regards,*
Bipin Singh
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