[gmx-users] RE: Cut off problem

Dallas Warren Dallas.Warren at monash.edu
Mon May 7 07:10:28 CEST 2012

Are you running constant pressure?  If so, not surprising the box is shrinking, since it is a vacuum.  You should use constant volume.

Also, you cannot change the values of those settings you have within the .mdp unless you have a good reason to and/or it is allowable by the forcefield.  These have particular values as defined by the forcefield, and you need to use those.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Anik Sen
Sent: Monday, 7 May 2012 2:55 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Cut off problem

Dear Gromacs users,

I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.
I want to see the interaction between some small atoms keeping them inside a periodic box without adding any solvent; i.e interaction between the atoms in the vacuum.
I have a total of 18-25 atoms in my system. The initial minimization was ok, but in case of the MD run, the job is failing after a few steps with the error,
Fatal error:
"One of the box vectors has become shorter than twice the cut off length or one of the box diagonal element has become smaller than cut off".
I have already changed the 'd' and 'rlist'; rvdw' and rcoulomb' to a number of different values to overcome the problem, but the problem persists.
How can I overcome this problem.

Thanking you in advance
Anik Sen
Anik Sen
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[Image removed by sender. www.csmcri.org]
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