[gmx-users] problem with interaction energy calculated by g_energy

Dear gmx users, I am studying the adsorption behavior of a molecule ( molecule 1) on a surface (molecules 2). Based on the production run, I calculated the interaction energy between molecule 1 and molecules 2 by g_energy. Here comes the first question: Why only short range interactions

[gmx-users] g_rms warning

Hi everyone, please I just need a precision: I need to calculate the RMSD of a trajectory by comparing it to a reference structure that doesn't have the same number of atoms. Gromacs is calculating the RMSD, but meanwhile it generates this warning:topology has 4839 atoms, whereas trajectory has

Re: [gmx-users] g_rms warning

Hi Carla, You'll have to use index groups to extract a trajectory and reference that correspond. If you have those you can get on with the RMSD. Cheers, Tsjerk On Mon, Mar 8, 2010 at 11:44 AM, Carla Jamous carlajam...@gmail.com wrote: Hi everyone, please I just need a precision: I need to

[gmx-users] mdrun_d not running in parallel

Hi , I had installed gromacs4.0.7 in double preicision in 64 bit Mac 10.6.1 computer with 8 dual core processors. 1) I installed the fftw-3.0.1 in the following way ( in the directory) ./configure --enable float sudo make sudo make install make distclean

[gmx-users] Re: AMBER force fields for ATP

No intrusion, but I have forwarded this to the GROMACS mailing list as all correspondence is best kept there. It gives you have a much greater chance of getting (better) help. The information needed for the parameters is best obtained from the supporting information given with the Carlson

Re: [gmx-users] Subtraction of xpm files

Itamar Kass wrote: Hi, I have calculated the Contact Maps of two proteins (WT and mutated one) and wish to compare the output XPM files. I thought the easiest way is to subtract the WT CM from the mutated proteins CM. I wonder if someone had done it and if so, is there any script to do so?

Re: [gmx-users] mdrun_d not running in parallel

sarbani chattopadhyay wrote: Hi , I had installed gromacs4.0.7 in double preicision in 64 bit Mac 10.6.1 computer with 8 dual core processors. 1) I installed the fftw-3.0.1 in the following way ( in the directory) ./configure --enable float sudo make sudo make install make distclean

[gmx-users] intrinsic viscosity

Hi All: I am using Gromacs 4.0.2 for the MD simulation of carbohydrates and I am trying to compute the intrinsic viscosity of them. Can I have it whith same gromacs programs? Sameone has experience about this? Any help would be appreciated Carmen -- gmx-users mailing list

[gmx-users] large number of molecules

Hello, I simulate carbon nanotube and basically I follow up http://cs86.com/CNSE/SWNT.htmBut when I increase the number of molecules (like 15000) , it gives me wrong results.Do you know why this is happen? Thank you,Kasim

RE: [gmx-users] large number of molecules

You are going to have to provide a lot more details than that if you want some help. What is wrong results? What is your input (copy and paste some commands in)? What is the output (copy and paste)? What makes you think the results are wrong? In what situations are they right? ... and

Re: [gmx-users] mdrun_d not running in parallel

- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Monday, March 8, 2010 23:33 Subject: Re: [gmx-users] mdrun_d not running in parallel To: Discussion list for GROMACS users gmx-users@gromacs.org sarbani chattopadhyay wrote: Hi , I had installed gromacs4.0.7 in

[gmx-users] reading xtc,trr and edr files

Hello, Is there any links to check or commands to read the xtc,trr and edr files for our analysis (writing our own scripts)? What are the format of data in these files for reading them? Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] intrinsic viscosity

- Original Message - From: ceste...@unsl.edu.ar Date: Tuesday, March 9, 2010 0:12 Subject: [gmx-users] intrinsic viscosity To: gmx-users@gromacs.org Hi All: I am using Gromacs 4.0.2 for the MD simulation of carbohydrates and I am trying to compute the intrinsic viscosity of them.

Re: [gmx-users] reading xtc,trr and edr files

Please search the webpage. There's a solution for writing your own C tools already. Mark - Original Message - From: Paymon Pirzadeh ppirz...@ucalgary.ca Date: Tuesday, March 9, 2010 9:42 Subject: [gmx-users] reading xtc,trr and edr files To: gmx-users@gromacs.org Hello, Is there any

Re: [gmx-users] problem with interaction energy calculated by g_energy

- Original Message - From: Qiong Zhang qiongzhang...@yahoo.com Date: Monday, March 8, 2010 20:35 Subject: [gmx-users] problem with interaction energy calculated by g_energy To: gmx-users@gromacs.org --- | Dear gmx users, I am

RE: [gmx-users] large number of molecules

My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover for Tcouple.and the beginning of mdp code looks like: ; RUN CONTROL PARAMETERSintegrator = md; Start time and timestep in pstinit= 0dt = 0.0005nsteps

Re: [gmx-users] large number of molecules

ksm tprk wrote: My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover for Tcouple. and the beginning of mdp code looks like: Partial information is useless. Post the whole .mdp file; there are plenty of parameters that can be set incorrectly or inconsistently.

Re: [gmx-users] large number of molecules

I wonder what's going on here: ; Groups to couple separately tc-grps = T1 T2 T3 T4 T5 T6 T7 ; Time constant (ps) and reference temperature (K) tau_t= 40 0 0 0 0 0 0 40 ref_t= 320 0 0 0 0 0 280 So you have multiple parts of your system at

Re: [gmx-users] large number of molecules

ksm tprk wrote: And one more thing. I change morse = no to yes but it was not good too. Do you know why morse does not work? The morse option corresponds to a Morse bond potential, which may or may not be appropriate for use with whatever force field you're using (which you haven't

Re: [gmx-users] large number of molecules

Hi Karim, On Mon, Mar 8, 2010 at 18:11, Justin A. Lemkul jalem...@vt.edu wrote: ksm tprk wrote: My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover for Tcouple. and the beginning of mdp code looks like: Partial information is useless.  Post the whole .mdp file;

[gmx-users] g_mindist output

Hi gmx users, I was running g_mindist as a batch job for a big number of files on a pbs cluster. The huge amount of output was redirected to the error file which has a size limit. Is there way to discard the output of g_mindist. I tried /dev/null as below, it didn't work. g_mindist -f tra.pdb -n

Re: [gmx-users] g_mindist output

Dian Jiao wrote: Hi gmx users, I was running g_mindist as a batch job for a big number of files on a pbs cluster. The huge amount of output was redirected to the error file which has a size limit. Is there way to discard the output of g_mindist. I tried /dev/null as below, it didn't work.

Re: [gmx-users] g_mindist output

Thank you, Justin. On Mon, Mar 8, 2010 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dian Jiao wrote: Hi gmx users, I was running g_mindist as a batch job for a big number of files on a pbs cluster. The huge amount of output was redirected to the error file which has a size limit.

[gmx-users] Re: mdrun_d not running in parallel

Message: 1 Date: 8 Mar 2010 11:49:40 - From: sarbani chattopadhyay sarbani_...@rediffmail.com Subject: [gmx-users] mdrun_d not running in parallel To: gmx-users@gromacs.org Message-ID: 20100308114940.35527.qm...@f5mail-236-242.rediffmail.com Content-Type: text/plain; charset=utf-8 Hi

Re: [gmx-users] g_mindist output

On 9/03/2010 12:22 PM, Justin A. Lemkul wrote: Dian Jiao wrote: Hi gmx users, I was running g_mindist as a batch job for a big number of files on a pbs cluster. The huge amount of output was redirected to the error file which has a size limit. Is there way to discard the output of g_mindist.

Re: [gmx-users] intrinsic viscosity

On 3/8/10 11:44 PM, Mark Abraham wrote: - Original Message - From: ceste...@unsl.edu.ar Date: Tuesday, March 9, 2010 0:12 Subject: [gmx-users] intrinsic viscosity To: gmx-users@gromacs.org Hi All: I am using Gromacs 4.0.2 for the MD simulation of carbohydrates and I am trying to