[gmx-users] Change to umbrella sampling pull code
jalemkul at vt.edu
Wed Aug 12 22:27:05 CEST 2015
On 8/12/15 3:20 PM, Nash, Anthony wrote:
> Hi Mark,
> Thanks for the reply.
> Comparing the documentation between manual-4.5.6 (what I had previously
> been using) and manual-5.0.4:
> 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there
> is no explicit mention (that I can see) to a reference group but there is
> one for the pull group (pull-group1-name).
Right, because multiple reaction coordinates can now be simultaneously be
restrained. There is no requirement for a single reference group. Any
combination of groups can be used. Offhand, your settings are right except
pull-ngroups is 2, as there are two groups.
> Dr Anthony Nash
> Department of Chemistry
> University College London
> On 12/08/2015 19:35, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>> On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>>> Dear all,
>>> This is the first time I¹ve ran pull code (for umbrella sampling) since
>>> the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in
>>> the .mdp key-value parameters. Could I have a sanity check on the values
>> I have no real idea, but you could start by comparing the respective
>> documentation. If something's not clear, that's something to fix ;-)
>> Also, given that I want a harmonic potential between the two
>>> groups, does it matter which index group is assigned to the respective
>>> Œpull-groupN-name¹ key?
>> I doubt it, but if you want a definitive answer, make yourself a toy test
>> case and see.
>>> Note: my reaction coordinate was defined initially following the
>>> trajectory between two minima during a meta-dynamics MD simulation. That
>>> too was distance based.
>>> ;Pull code
>>> pull = umbrella
>>> pull-geometry = distance
>>> pull-dim = Y Y Y
>>> pull-start = yes
>>> pull-ngroups = 1
>>> pull-group1-name = ZINC
>>> pull-group2-name = CARBONYL
>>> pull-coord1-init = 0
>>> pull-coord1-rate = 0
>>> pull-coord1-k = 1000
>>> pull-nstxout = 1000 ; every 2 ps
>>> pull-nstfout = 1000 ; every 2 ps
>>> Many thanks
>>> Gromacs Users mailing list
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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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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