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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Anik Sen Sent: Monday, 7 May 2012 2:55 PM To: gmx-users@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 Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [Image removed by sender. www.csmcri.org] ========================================================
<<inline: ~WRD000.jpg>>
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
