[gmx-users] infinite force at the membrane lipid
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Sun Aug 16 13:21:59 CEST 2015
How did you construct your membrane, with CHARMM-GUI? What is the lipid? From my experience, I have found that sometimes CHARMM-GUI does not provide a good starting point for MD. So I would suggest you to :
- center the lipids inside the box to have no lipids that cross the box limit and/or increase a little bit the box size (x-y) and minimize your system again.
Moreover to insert you protein inside the membrane, did you try the inflate_gro or g_membed tools ?
Date: Sun, 16 Aug 2015 10:51:42 +0900
From: Vy Phan <phanvy120690 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] infinite force at the membrane lipid
<CAC+3Te00hidSrXE49g5mfqvCsBSaE5wTJ-NtFubaXvvz=U68+g at mail.gmail.com>
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Dear Dr Justin and Gromacs User,
This is my commands for running energy minimization.
define = -DPOSRES
integrator = cg
nstcgsteep = 1000
emtol = 100.0
emstep = 0.01
dt = 0.002
; Output control
nstxout = 50
nstenergy = 50
nstlog = 50
nstlist = 1
cutoff-scheme = Verlet
ns_type = grid
coulombtype = PME
rcoulomb = 1.2
vdw-modifier = Potential-shift
rvdw = 1.2
rvdw-switch = 1.0
pbc = xyz
I hope you can give more recommendations. Removing lipids actually is not
an appropriate solution.
Thank you so much
2015-08-16 1:47 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:
> On 8/15/15 12:41 PM, Vy Phan wrote:
>> Dear All gromacs Users,
>> I want to run the membrane protein simulation. I run the energy
>> minimization for membrane and protein separately.
>> After that I combine protein and lipid together and remove the
>> when I run energy minimization I got the error "inf at atom on lipid". I
>> remove the lipid which includes this atom. I got the error several time
>> and I repeat remove lipid. I see the "inf at atom on lipid" always happens
>> on lipids which locate at the wall (at the boundary of unit cell).
>> I successfully run one time when I remove lipids have error, another was
>> I wonder why the error "inf at atom on lipid" always happens on lipids
>> which locate at the wall. Maybe I did something wrong about periodic
>> boundary condition.
>> Thank you for any thoughts.
> Without a list of your exact commands and what you've done to this point,
> it's impossible to diagnose. There's something fundamentally wrong with
> the coordinates, topology, or both. If the infinite force is just moving
> around, what you're observing is a symptom, not a cause, and removing
> lipids to try to make it go away is not an appropriate solution.
> 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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