[gmx-users] umbrella sampling tutorial

[Ming Tang]

Dear Justin,

I have tried many cases, and only your code runs smoothly. If I set pull-ngroups = 1, it will warn that pull-group2-name= Chain_A has not been defined.
The code you gave me last time runs well. Though the COM between Chain_A and Chain_B remains the same over time, I found that Chain_A does dissociate from the structure and some particles fly away.
I am trying from the beginning once again and hope to find the reason. Besides, I got another problem. I want to probe the mechanical properties of a triple helix. 
I tried to fix one side (End) and pull the other side using the umbrella method:

; freeze groups
freezegrps      = End
freezedim       = Y Y Y

; COM pulling
pull                = umbrella
pull-geometry       = distance
pull-dim            = Y N N
pull-start          = yes
pull-ngroups        = 2
pull-ncoords        = 1
pull-coord1-groups  = 1 2
pull-group1-name    = End
pull-group2-name    = pull
pull-coord1-rate    = 0.005
pull-coord1-k       = 1000

WARNING: Listed nonbonded interaction between particles 179 and 190 at distance inf which is larger than the table limit 2.437 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

If I just fix one of the three dimensions, it can run around 100 steps. Then, I turned to use SMD method to pull the triple helix along x direction. I tried the following method to generate the box, but got a fatal error.
editconf -f complex.gro -o newbox.gro -c -d 1
editconf -f complex.gro -o newbox.gro -center 5.63865 1.8837 1.9762 -box 20 3.8 4.0

; freeze groups
freezegrps      = End
freezedim       = Y Y Y

; COM pulling.
pull                = umbrella
pull-geometry       = direction-periodic
pull-start          = yes
pull-ngroups        = 2
pull-ncoords        = 1
pull-coord1-groups  = 1 2
pull-group1-name    = End
pull-group2-name    = pull
pull-coord1-rate    = 0.01
pull-coord1-k       = 1000
pull-coord1-vec     = 1 0 0

Fatal error:
Can not have dynamic box while using pull geometry 'direction-periodic' (dim x)

Could you teach me how can I build a fixed box? And is my SMD code right?  

Thanks,
Ming

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Friday, 13 March 2015 10:57 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/12/15 8:49 PM, Ming Tang wrote:
> Dear Justin,
>
> I switched Chain_A and Chain_B in the .mdp file, but got the same result.
> In the tutorial:
> pull-ngroups: (1)
> The number of pull groups, not including the absolute reference group, when used. And we need to assign the Chain_B as the reference group.
>

So does this mean things are working if you set pull-ngroups = 1 (which it should have been)?

-Justin

--
==================================================

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 http://mackerell.umaryland.edu/~jalemkul

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