Re: [gmx-users] (no subject)

http://www.gromacs.org/Support You're emailing a list of Gromacs users and developers; compose your question as you would any other email. -Justin On 4/26/14, 10:17 PM, Swetha Srinivasan wrote: Hi, I don't know how to post my queries.Could you help me with that. Thanks, Swetha __

Re: [gmx-users] (no subject)

Hi, I don't know how to post my queries.Could you help me with that. Thanks, Swetha From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Swetha Srinivasan Sent: Saturday, April 26, 2014 10:14 PM To: gromacs.org_gmx-users@maillist.sys.k

[gmx-users] (no subject)

Hi, My mail id is ssrin...@syr.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.

Re: [gmx-users] High Pressure with Martini system

Hi Ricardo, You can also use insane to build an initial model of the membrane+protein+solvent, and then solvate that system in a larger box. If you then run with position restraints on the membrane and the protein, you should be fine, being able to equilibrate the system, without distorting the pr

Re: [gmx-users] High Pressure with Martini system

Hello Tsjerk, I found out the the big frozen membrane was causing the extremely large pressure, so now I made a box with the same previous dimensions, now filled with only W water and ions. The system is running fine. After this step, I'm going to convert W to PW and further equilibrate it.The

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

On 4/26/14, 8:42 AM, Andrew Bostick wrote: Dear Justin Thanks for your reply. This problem can be solved by changing the parameters related to file system ? Well, you could, but that would require reformatting your file system for something that can handle file size > 2 GB. If I add

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Justin Thanks for your reply. This problem can be solved by changing the parameters related to file system ? If I add another RAM to my computer system, my problem solves? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

Re: [gmx-users] Help regarding potential energy

On 4/26/14, 6:05 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote: Dear Gromacs users, I am doing a protein-peptide simulation using gromos43a1 forcefield (as per the tutorial) When i do the energy minimization step before beginning equilibration, I get the following results: Steepes

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

On 4/26/14, 4:54 AM, Andrew Bostick wrote: Dear Mark I'm apologize. You are right. I should give more indication and information you to help me. I used chmod -R 777 directory containing pdb and mdp files. Then I did MD simulation again: (pdb2gmx ...> editconf > em ...> npt eq ...> m

[gmx-users] Help regarding potential energy

Dear Gromacs users, I am doing a protein-peptide simulation using gromos43a1 forcefield (as per the tutorial) When i do the energy minimization step before beginning equilibration, I get the following results: Steepest Descents converged to Fmax < 1000 in 652 steps Potential Energy = -8.042348164

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark I'm apologize. You are right. I should give more indication and information you to help me. I used chmod -R 777 directory containing pdb and mdp files. Then I did MD simulation again: (pdb2gmx ...> editconf > em ...> npt eq ...> md) My problem is in md step (md.trr file). 1)