[gmx-users] Pull code

Justin Lemkul jalemkul at vt.edu
Thu Apr 23 13:43:45 CEST 2015

On 4/22/15 8:51 PM, Alex wrote:
> Okay, that clarifies it. I wasn't sure, because of your earlier comment,
> despite the fact that I was using referenced pull. Indeed, in my case, part
> of the system is essentially solid-state, its COM fixed in space, while
> other stuff is being moved relative to it.
> I was also curious how (in more detail than what the manual says) the
> periodic pull worked. I think I would greatly benefit from the ability to
> translocate, say, a strand of DNA infinitely across a periodic boundary. As
> is, that would never work, because the group's COM would be nearly static,
> eventually resulting in huge forces applied to the pulled group. So, if the
> periodic option is used, will it be possible to continuously translocate a
> linear chain with a length comparable to the corresponding box dimension,
> while the rest of the system is non-translating?

No idea, never tried it.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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