[gmx-users] Increase the box size or decrease rlist

[Justin Lemkul]

On 8/19/14, 2:14 PM, pragna lakshmi wrote:
> Dear all,
> I am trying to do MD simulation of POPC membrane simulation with peripheral
> attachment of protein ligand complex. Steps that i have performed so far
> are:
>
> 1. orienting the protein with editcong -princ command
> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command
> 3. separation of protein ligand files into individual files and generation
> of topology file of protein from pdb2gmx and ligand from swissparam.
> (charmm 36ff was used for protein topology generation. source:
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs )
> 4. The protein and ligand files were merged followed by necessary changes
> in topology file.
> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's website
> whereas its itp file was taken from Stockholm_Lipids website.

The Stockholm lipids are derived from Amber force fields.  You can't combine 
them with CHARMM protein parameters and expect anything physically meaningful. 
If you're using the CHARMM protein force field, use the CHARMM lipid parameters.

> 6. After this, when i am running the command
> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr
> i am facing the fatal error:
> ERROR: The cut-off length is longer than half the shortest box vector or
>    longer than the smallest box diagonal element. Increase the box size or
>    decrease rlist.

What are the box vectors listed in POPC.gro?

> As it is suggesting, I have decreased rlist, rcoulomb and rvdw from 1.2 to
> 1.0. But still the same error is raising.

Don't mess with these settings just to make an error message go away.  The 
nonbonded setup is a fixed feature of the force field, and lipids are especially 
sensitive to changes here.  I just posted the proper settings for the CHARMM 
force field a few days ago; use those settings and don't deviate unless you have 
proof that what you're doing is superior.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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