[gmx-users] errors position restraints in a linux cluster

[gerph at correo.unam.mx]

Dear all,

recently, I get access to a linux-cluster in my university to run gromacs,
however, after a few days of test, with errors, I saw that the administers
installed gromacs 3.1.1. Previusly I did a test with my protein in a single
linux workstation with gromacs 3.2.1 without problems and then I tried run the
same MD steps in the cluster but I am having the next problem with position
restraints and Na,

Back Off! I just backed up mdout.mdp to #mdout.mdp#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
WARNING 1 [file /home/inv/evqz/beta/300K/pr.mdp, line unknown]:
  Can not do sorting without shuffling. Sorting turned off.
Excluding 3 bonded neighbours for Protein_E 1
Excluding 1 bonded neighbours for SOL 27509
Excluding 1 bonded neighbours for Na 20
processing coordinates...
Reading file /home/inv/evqz/beta/300K/tbeta_em.tpr, VERSION 3.1.1 (single precision)
Reading file /home/inv/evqz/beta/300K/tbeta_em.tpr, VERSION 3.1.1 (single precision)
Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
/home/inv/evqz/beta/300K/tbeta_em.tpr don't match (OW - Na)

Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
/home/inv/evqz/beta/300K/tbeta_em.tpr don't match (HW1 - Na)

its look the same for the rest of Na

I am using gromacs force field and I add #include "ions.itp" in the top file as
well as I arranged the lines of n ions by solvent before run grompp.
I need upgrade to 3.2.1?
I appreciate any insights about this problem. 

Thanks in advance,

Gerardo Pérez-Hernández

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