[gmx-users] MD after equilibration phase

[bipin singh]

Thanks for your comments
 I have a very crude question which may not be even logical to ask here but
I just want to know your opinion on this:

If I will perform two simulations in following two ways :

*RUN:1*

(1) Did NVT with POSRES on protein and
    gen_vel=yes
    gen_temp= 350

(2) Did NPT with POSRES on protein and
    continuation=yes
    gen_vel=no ;Without reading velocities from NVT

(3) Did MD with No POSRES (NPT)
     continuation=yes
     gen_vel=no ; No velocities read from previous run


*
RUN:2

*(1) Did NVT with POSRES on protein and
    gen_vel=yes
    gen_temp= 350

(2) Did NPT with POSRES on protein and
    continuation=yes
    gen_vel=no ; Reading velocities from NVT run using -t option

(3) Did MD with No POSRES (NPT)
     continuation=yes
     gen_vel=no ; Velocities read from previous run using -t option



What will be the expected flaws of the RUN:1 over RUN:2 and will the
results got from the RUN:1 is unreliable ? If yes why ?



On Fri, Apr 6, 2012 at 20:26, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> On 7/04/2012 12:37 AM, Justin A. Lemkul wrote:
>
>>
>>
>> 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.
>>
>
> It's conceivable that there are velocities in a mdrun -c
> finalstructure.gro file, but these would have to be only at low precision,
> and thus often useless.
>
> Mark
>
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-- 
-----------------------
*Regards,*
Bipin Singh
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