On 11/10/13 5:31 AM, shahab shariati wrote:
Dear Justin

Thanks for your reply.

You are right. I should  not extrapolate too literally from your tutorial
to my system.

But, I have a general question:

There is 2 groups in COM pulling method (reference group + pull group).

If I want to use pull_geometry = distance, so, I should fix reference group
to be immobile. Is it true?

What you described earlier should not be attempted with "distance" geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group.

On the other hand, I want to know exactly using position restraining on
reference group is optional or mandatory in COM pulling method?

Almost never used.  More explicitly - you do not need position restraints.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

gmx-users mailing list    gmx-users@gromacs.org
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to