[gmx-users] About the data loss due to Disk space problem

Dear Gromacs Users, I am facing the problem with the output generated during the condition of critical disk space (Both Hard disk and OS associated Memory space). The problem definition is as follows: 1. The .trr and .xtc file generated shows Incomplete frame error in the very beginning of the

[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp

ns_type = grid rlist = 1.2 coulombtype = pme vdw-type = cut-off rvdw = 1.2 rcoulomb = 1.2 ; ; Energy Minimization Stuff ; ; emtol = 0.001 emstep = 0.01 Thanking you in advance . Regards, Pavan Payghan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option

with semiisotropic couple type is wrong method or no such problem? Please suggest me whether to move ahead with ignorance to the warnings or to change some parameters in mdp file? I have attached my npt.mdp file for your consideration. Thanking you In advance, Pavan Payghan npt.doc Description: MS

[gmx-users] gmx-users Digest, Vol 98, Issue 42

/tutorial (including Bevans Lab ) suggesting the position restraining of protein during NVT as well as NPT. That is the reason I have followed the same. Please clarify your view on this matter. Thak you very much in advance. Pavan Payghan On Thu, Jun 7, 2012 at 4:58 PM, gmx-users-requ

[gmx-users] Re: gmx-users Digest, Vol 96, Issue 189

Dear Mark, Thanks a lot for the reply and highlighting the cause of error that I was facing. Still can it be possible to overcome the same error with the available facility. Pavan Payghan On Thu, Apr 26, 2012 at 9:55 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list

[gmx-users] How to increase the ratio of cell size to constrain length per error message

Dear Gromacs Users, I am using gromacs version is 4.5.3. and running my jobs on single node with 8 cores. I have two different systems which contain about 425000 atoms (protein + Lipid +SOL) one with bound ligand and another one unbound protein. I have successfully reached up to NPT

[gmx-users] Re.Importance of -rcon and -dd options when

mark.abra...@anu.edu.au Subject: Re: [gmx-users] Importance of -rcon and -dd options when using mdrun with mpi. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f608d4e.10...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 14/03/2012 9:54 PM, PAVAN

[gmx-users] Importance of -rcon and -dd options when using mdrun with mpi.

Dear Gromacs Users, I am running mdrun on single node with 8 CPU and getting following error Fatal error:- D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are connected via constraints from the neighbouring cells. This probably means your constraint length are too long compared

[gmx-users] Atom Type not found............

HI i have generated a topology file for drug using prodrg with gromos 96.1force field , now i want to use it for simulation with DNA in complex. I am using amber 03 force field for my system . i have included correctly the drg.itp file in generated topology file for DNA alone (using pdb2gmx). i

[gmx-users] Regarding Trjconv.and ligand -protein complex simulation.......

Thnx for replying A] As i hv mentioned previously that in my simulation g_rms suggests it has some large peaks ,so applied trjconv with -pbc nojump now ... there are no peaks in rmsd its oky but in vmd it showed that water is not having defined box so how to tackle this situation.. 1.which

[gmx-users] HI

I have to recreate .gro file from .trr file by using trjconv which i have deleated previously for disk space reasons , im using following commond for that trjconv -f full.trr -s full.tpr -o fullout.gro . so my question is will this commond give me the same gro file that it

[gmx-users] restartng run..........

HI I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to

[gmx-users] restartng run..........

only molecule of interest . also while choosing groups is it correct to choose both time i.e. for least square fitting and RMSD same groups. Thanking you in Advance. Mr. Pavan Payghan INDIAN INSTITUTE OF CHEMICAL BIOLOGY KOLKATA -- gmx-users mailing listgmx-users

[gmx-users] Incomplete frame,while running trjconv .....

HI i have to create .xtc file to save my disk space,but while i was running it using trjconv i got warning message incomplete frame.Actually i was running my system on four nodes with mdrun_mpi but it stopped due to unavailability of disk space so from this it is certain that my

[gmx-users] water molecule not settled.........

hi ... while running mdrun im getting an error water molecule is not settled there is only single such water molecule what should be possible way out...? the same system when i run in previous version of gromacs it showed wrote pdb files with previous current