[gmx-users] Pull code

Alex nedomacho at gmail.com
Thu Apr 23 02:51:49 CEST 2015

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?

Thanks as always.


On Wed, Apr 22, 2015 at 6:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 4/22/15 8:37 PM, Alex wrote:
>> That is not an option for me, all groups must exhibit full dynamics, so
>> partial restraint seems like a decent option.
>> It is my understanding that explicitly moving only one group is impossible
>> in the new version. Is that the case?
> No, you can (and have always been able to) use an absolute restraint
> relative to the coordinate origin.  There are additional complications in
> this case (noted in the manual), so it's not often used.  The current setup
> that you're using is such that one group is moved with respect to the
> other.  So in effect, you are "moving only one group" but its position
> depends on the other.  In most cases, the absolute position of the
> reference group is irrelevant, though not always.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
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