[gmx-users] Visualization of .trr problem in VMD

Dear All I am working on protein unfolding simulation in gromacs. when I do a production run on 32 node HPC I get .trr file along with .gro. when I try to visualize this files in VMD I see erratic large movement of atoms in the trajectory. With same .mdp files when I did smaller run of 2ns on sing

[gmx-users] Can gromacs be compiled for "openmp"

Hi everyone, Can gromacs be compiled for "openmp" Due to use mulitcore processors, so I am interested in how to compile with openmp. Thanks and regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Visualization of .trr problem in VMD

shahid nayeem wrote: Dear All I am working on protein unfolding simulation in gromacs. when I do a production run on 32 node HPC I get .trr file along with .gro. when I try to visualize this files in VMD I see erratic large movement of atoms in the trajectory. With same .mdp files when I did s

Re: [gmx-users] Can gromacs be compiled for "openmp"

On 4/3/10 1:08 PM, lina wrote: Hi everyone, Can gromacs be compiled for "openmp" Due to use mulitcore processors, so I am interested in how to compile with openmp. Thanks and regards, lina There is no openmp implementation of mdrun in gromacs. The upcoming version 4.5 will have a threaded im

[gmx-users] Re: gmx-users Digest, Vol 72, Issue 13

Hi, I tried to use 4 and 8 CPUs. There are about 6000 atoms in my system. The interconnect of our computer is the network with speed 1Gb but not optical fiber. I'm sorry for my poor English and I couldn't express well in my question. Everytime I submitted the parallel job, the nodes assigned to

[gmx-users] g_sas

Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

Re: [gmx-users] g_sas

Chih-Ying Lin wrote: Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Please consult the documentation. From g_sas -h: "The program will ask for a grou

Re: [gmx-users] g_sas

On 4/3/10 8:36 PM, Justin A. Lemkul wrote: Chih-Ying Lin wrote: Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Please consult the documentation. From g_s

[gmx-users] problem with total energy

Dear Berk, I am sorry if i am confusing you with my poor description of problem, actually I have submitted simulation with two temperature coupling groups (i think you already know that from our earlier conversations) and found that there is a continuous increase in the total energy of the system.

[gmx-users] DSSP => how to edit .eps file

HI After running DSSP, .eps files are created. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? Also, how can I change the thickness of the color band for each residue? The logo indicates the co

Re: [gmx-users] DSSP => how to edit .eps file

Chih-Ying Lin wrote: HI After running DSSP, .eps files are created. No they aren't; you create .eps files from the .xpm output that do_dssp generates. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues.

Re: [gmx-users] DSSP => how to edit .eps file

On 4/3/10 9:19 PM, Justin A. Lemkul wrote: Chih-Ying Lin wrote: HI After running DSSP, .eps files are created. No they aren't; you create .eps files from the .xpm output that do_dssp generates. We can see the second structures of the all residues. I only want to see the change of the sec

Re: [gmx-users] Re: gmx-users Digest, Vol 72, Issue 13

On 4/04/2010 3:13 AM, Hsin-Lin Chiang wrote: > Hi, > > I tried to use 4 and 8 CPUs. > There are about 6000 atoms in my system. > The interconnect of our computer is the network with speed 1Gb but not > optical fiber. Gigabit ethernet is too slow for good scaling of GROMACS beyond about 2 or 4 cp

[gmx-users] Potential Tables for user defined potentials

Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately?

Re: [gmx-users] Potential Tables for user defined potentials

Sikandar Mashayak wrote: Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and flui

[gmx-users] Re: insert silicon atoms into ice structure

Thanks for reply. I intended to add these silicon atoms into ice structure, the Santan William wrote: > Dear GMXusers, > I wanna insert several silicon atoms into an ice crystal. I use > genbox with a Silicon.pdb, but there's no any silicon atom in the out > file. Do I miss anything? Anyo

[gmx-users] Re: insert silicon atoms into ice structure (Justin A. Lemkul)

Thanks for reply. I intended to add some silicon atoms just into ice structure, so the simulation box only containing ice. You said there probably isn't enough space for them in the box. Did you mean I can't insert these atoms into ice structure if the box only containing ice? Is there any other wa

Re: [gmx-users] Re: insert silicon atoms into ice structure (Justin A. Lemkul)

Santan William wrote: Thanks for reply. I intended to add some silicon atoms just into ice structure, so the simulation box only containing ice. You said there probably isn't enough space for them in the box. Did you mean I can't insert these atoms into ice structure if the box only containi

[gmx-users] DSSP=> how to edit .eps file

HI 1. dssp -n index.ndx => only atom numbers of one residue in the index.ndx => can dssp decide the exact second structure for the only one residue without considering other residues of protein? => can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n p

[gmx-users] g_sas

HI THe command => g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg => @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "Total" @ s3 legend "D Gsolv" What does "Hydrop

Re: [gmx-users] DSSP=> how to edit .eps file

On 2010-04-04 06.40, Chih-Ying Lin wrote: HI 1. dssp -n index.ndx => only atom numbers of one residue in the index.ndx => can dssp decide the exact second structure for the only one residue without considering other residues of protein? no. => can i get the same second structure for the res