Re: [gmx-users] gromacs installation on Vista

maryam zargarzadeh wrote: I would like to know if I can install gromax on vista and the procedure. Start by searching the GROMACS webpage. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] energy minimization

subarna thakur wrote: I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ;Energy minimizing

Re: [gmx-users] Reproducing Chain Tilt on DPPC gel phase with Martini FF

On Dec 9, 2009, at 11:21 PM, César Ávila wrote: Dear all, I would like to simulate a DPPC membrane in gel phase using Martini Force Field. As stated on Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model, CPL 135 (2005) 223-244 the correct 30º

Re: [gmx-users] energy minimization

Hello Can increase the emtol from 1000 to 1 KJ mol - 1 nm-1?   subarna From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, 10 December, 2009 2:33:23 PM Subject: Re: [gmx-users] energy minimization

[gmx-users] how to plot free enenrgy landscape and exact corresponding conformation

Dear Users of Groamcs: ON the abasis of ED analysis, how to plot free energy landscape and exact corresponding conformation? Thank you very much! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/-- gmx-users mailing list

Re: [gmx-users] how to plot free enenrgy landscape and exact corresponding conformation

On 12/10/09 11:11 AM, xi zhao wrote: 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844Dear Users of Groamcs: ON the abasis of ED analysis, how to plot free energy landscape and exact corresponding conformation?

Re: [gmx-users] energy minimization

subarna thakur wrote: Hello Can increase the emtol from 1000 to 1 KJ mol ^- 1 nm^-1? I wouldn't recommend it. That would be a really large maximum force, which would probably cause your system to be very unstable. Look at your original structure to see what might be wrong instead of

Re: [gmx-users] New to Gromacs -- looking for insights

Thanks for the help. On 12/09/2009 05:57 PM, Mark Abraham wrote: Simone Pellegrini wrote: Dear all, I am researching optimization for MPI parallel programs. As I saw Gromacs seems to use MPI and my idea is to test some of the program transformations I am aware of to improve the performance.

Re: [gmx-users] How to increase nodes in mdrun option

Mahendran E wrote: hi all while running gromacs in parallel environment i am getting the following command, the command i used is mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr error: Program

Re: [gmx-users] How to increase nodes in mdrun option

Mahendran E ha scritto: hi all while running gromacs in parallel environment i am getting the following command, the command i used is mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr error:

[gmx-users] How to increase nodes in mdrun option

hi all while running gromacs in parallel environment *mpirun -np 3* -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr *for mpirun 3 nodes i got the output,* while trying to increase the nodes to 5 or 8 i am getting the

Re: [gmx-users] How to increase nodes in mdrun option

Mahendran E wrote: hi all while running gromacs in parallel environment *mpirun -np 3* -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr *for mpirun 3 nodes i got the output,* while trying to increase the nodes to

[gmx-users] some questions about umbrella sampling

Dear All: I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce enough

[gmx-users] some questions about umbrella sampling

I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. why not gmx 4? In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce

[gmx-users] g_velacc problem

Hi all, I am trying to do velocity auto-correlation function(VACF) for the 'oxygen atom' present in a 63 Ang. cubic water box, simulated upto 500ps. And the velocities are stored at every 5fs. While doing the analysis(g_velacc), it got struck at 400ps, since if felt it is mainly due to the

Re: [gmx-users] mpispawn.c:303 Unexpected exit status

Hi Justin, Sorry about the email. I just made a mistake while posting. First of all, Thanks for replying. I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting the same error. I am attaching

Re: [gmx-users] fftw vs cmkl

Dallas B. Warren wrote: Thanks Mark. My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps fftw 3.2.1 - 20,027 seconds Intel cmkl - 19,792 seconds So about 1.2% faster. IIRC icc does a better job on mkl

[gmx-users] Msd of molecule center of mass (g_msd -mol with -rmcomm)

Hello, Does anyone have additional details about how the calculations are done for the -mol flag of g_msd when using -rmcomm? I am comparing results with and without the -mol flag. I presume that when -mol is used the file specified by the -o flag contains the average msd of the centers of mass

Re: [gmx-users] mpispawn.c:303 Unexpected exit status

shivkumar bale wrote: Hi Justin, Sorry about the email. I just made a mistake while posting. First of all, Thanks for replying. I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting

Re: [gmx-users] mpispawn.c:303 Unexpected exit status

Hi Justin, Thanks for replying. No .log file is produced. Can you elaborate what do you mean by ' this really sounds more like a job for your sysadmin '. What should I exactly do to rectify this error? I am new to super computers and gromacs. Regards Shivkumar On Thu, Dec 10, 2009 at 6:59 PM,

Re: [gmx-users] mpispawn.c:303 Unexpected exit status

shivkumar bale wrote: Hi Justin, Thanks for replying. No .log file is produced. Can you elaborate what do you mean by ' this really sounds more like a job for your sysadmin '. What should I exactly do to rectify this error? I am new to super computers and gromacs. If no output is

RE: [gmx-users] fftw vs cmkl

3D-FFT under both situations is 21.4% and PME mesh down as 54% (figures taken from the second last and last tables in the .log file, respectively). Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar

[gmx-users] splitting a trajectory

Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about it either by splitting the

Re: [gmx-users] splitting a trajectory

Ramachandran G wrote: Dear gromacs users: Can any one tell me how can i split a trajectory file from a specific time interval of my interest. For example if i have a trajectory file up to 0-100ps, and my interest is to consider part of the trajectory from 50-75ps, how i can go about

RE: [gmx-users] splitting a trajectory

Another option is to create a new trajectory file to use in your analysis, using trjconv Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From:

Re: [gmx-users] splitting a trajectory

Thanks for your help. I have tried the command trjconv -f traj.trr -s AFP-500ps.tpr -b 87001 -e 99000 -o test.gro but nothing was written on output file(test.gro) and got the message WARNING no output, trajectory ended at 500 Am i doing it right? On Thu, Dec 10, 2009 at 8:08 PM, Justin A.

Re: [gmx-users] splitting a trajectory

Ramachandran G wrote: Thanks for your help. I have tried the command trjconv -f traj.trr -s AFP-500ps.tpr -b 87001 -e 99000 -o test.gro but nothing was written on output file(test.gro) and got the message WARNING no output, trajectory ended at 500 Am i doing it right? Obviously not.