[gmx-users] Continuation=yes From?
ramezanpour.mohsen at gmail.com
Mon May 2 13:34:29 CEST 2011
Thank you for your reply
My is Protein-ligand,It is have the same conditions as tutorial.I did pull
ligand in the z direction.
Actualy I found your note about gen_vel ,but I didn't any about
You are right,But there is another problem:
You have not used any -t option in grompp command (doing umbrella
Since we have set Continuation=yes;
Can grompp realize from which .cpt (npt.cpt ) it must use ?
And my last question:
Do I need to any .cpt file ? (Because I have set Continuation=yes)
Thanks in advance
On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> mohsen ramezanpour wrote:
>> Dear Dr.Justin
>> Regarding Umbrella Sampling tutorial:
>> The CONTINUATION option in md_umbrella.mdp is YES,
>> and you have noticed : From NPT
>> I can't understand it's reason correctly!
> This is a meaningless comment. It was left there from copying and pasting
> files before modifying them. The important part is that "continuation =
> yes" be set to correctly solve the constraints.
> we run a NPT and then Pulling, then extracted some configurations from
>> pull.trr file.
>> I think we must continue from pull.cpt not NPT.cpt
>> I mean :
>> grompp -f md_umbrella.mdp ............................. -t pull.cpt
>> is more correct than
>> grompp -f md_umbrella.mdp .............................. -t NPT.cpt
>> am I right?
> In the case of the tutorial, no. There is not a corresponding .cpt file
> for each configuration generated. If you were to somehow apply the same
> .cpt file for each configuration, almost certainly some of the windows would
> blow up because the initial velocities would cause nasty collisions. Note
> that I discuss the continuation issue, proper settings for gen_vel, etc. in
> the tutorial, step six.
> Thanks in advance for your reply
> 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
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