[gmx-users] Continuation=yes From?

Justin A. Lemkul jalemkul at vt.edu
Mon May 2 12:57:16 CEST 2011

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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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