[gmx-users] infinite force at the membrane lipid

[ABEL Stephane 175950]

Hello,

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 ?

Good luck

HTH

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Message: 1
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
Message-ID:
        <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

Tuong Vy

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
>> overlapping
>> molecules.
>> 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
>> failed.
>>
>> 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
>
> --
> ==================================================
>
> 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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