[gmx-users] System Problem

Hello everyone I am using Gromacs 5.0 for running a tutorial. The tutorial is successfully done and i have obtained .gro file. I am a beginner and do not have idea how to visualize this file in pymol? can anyone help in this regard? Secondly, this may be a partition problem but if anyone knows,

Re: [gmx-users] problem to restart REMD

Hi, See mdrun -h regarding -cpt Mark On Sun, Jun 28, 2015 at 1:53 PM leila salimi leilasal...@gmail.com wrote: Dear Mark, I have a question about the updatedtate file, I run the simulation with 6 replicas now and the state*.cpt files are not updated after 1.5 ns and it seems strange for

Re: [gmx-users] problem to restart REMD

Dear Mark, I have a question about the updatedtate file, I run the simulation with 6 replicas now and the state*.cpt files are not updated after 1.5 ns and it seems strange for me! I would like to know how long the restart files are updated? Regards, Leila On Fri, Jun 26, 2015 at 9:49 PM, leila

[gmx-users] (no subject)

Hello dear friends I want to simulate a Ligand-Protein complex in GROMACS by using amber forcefield https://www.google.com/search?q=forcefieldnewwindow=1sa=Xbiw=1366bih=657tbm=ischtbo=usource=univei=WEaQVYH_AoWdsgH06q6ICgved=0CE4QsAQ and need essential MDP files. Can anyone provide me that files?

Re: [gmx-users] (no subject)

On 6/28/15 3:22 PM, Vidyalakshmi CM wrote: Hi, You may use the mdp files from the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ (It has topologies for energy minimzation, nvt and npt simulations and md simulations run). The tutorial .mdp settings

Re: [gmx-users] (no subject)

Hi, You may use the mdp files from the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ (It has topologies for energy minimzation, nvt and npt simulations and md simulations run). Regards, C.M.Vidyalakshmi On Sun, Jun 28, 2015 at 8:19 PM, masoud aliyar

Re: [gmx-users] (no subject)

*not topologies - mdp files On Sun, Jun 28, 2015 at 8:22 PM, Vidyalakshmi CM vidyalakshmi...@gmail.com wrote: Hi, You may use the mdp files from the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ (It has topologies for energy minimzation, nvt and

[gmx-users] end to end relative rotation of DNA

Dear gromacs users, I am stretching the COM of 2 first residues and 2 last residues of a DNA double helix using umbrella pulling method . Is there a command to calculate the relative rotation between both ends? thanks in advance. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Problem with gmx distance

Hi, I created an index files with two residue groups, 15 r 22 contains 15 atoms and 16 r 137 contains 24 atoms. Then, I use: gmx distance -s run.tpr -f run.xtc -n index.ndx -oall dist.xvg when I try to select both groups, I get this message Cannot match 'group 15', because no such index group can

[gmx-users] MD Sim stopped at 14 Ns

Dear GMX Users, I hav a MD sim for 20ns but due to sme powr outrage it stoppes at 14ns... Now the power is back. Is there any command to continue from 14 ns or else i have to start frm the begening. Yours sincerely PS Salam Tezpur University, Assam, India -- Gromacs Users mailing list * Please

[gmx-users] question

Dear Gromacs users, I am beginner in gromacs. I have a question. Can I do MD simulation of a proccess such as protein aggregation (not folding), fibrillogenesis and fibril formation of proteins? Is this possibility for such aims using Gromacs package? Any help will highly appreciated. --

Re: [gmx-users] MD Sim stopped at 14 Ns

Hi SP, Follow this link to continue your simulation. http://blog.sina.com.cn/s/blog_4d19911d01018c4a.html Thanks, Dhana On Mon, Jun 29, 2015 at 2:31 PM, salam pradeep salamprad...@gmail.com wrote: Dear GMX Users, I hav a MD sim for 20ns but due to sme powr outrage it stoppes at 14ns...

[gmx-users] Doubt on membrane patch

Dear Gromacs users . I am working on membrane simulations, I have replicted the membrane patch of DPPC128.pdb using genconf with nbox. However almost 512 lipids seems larger for my GPCR and takes long computational time. How can I adjust the numbdr of lipids to become 300 patch, before inflation