Re: [gmx-users] How to create a spherocylindrical wall

Hi This dates back to an old query on using restraints to create a spherocylindricalconfinement. a) Based on previous suggestions, we were exploring the options of flatbottomed potential. However, it has three options only: sphere, cylinder and layer. We wanted to create a combination of cy

Re: [gmx-users] How to create a spherocylindrical wall

Hi This dates back to an old query on using restraints to create a spherocylindrical confinement. a) Based on previous suggestions, we were exploring the options of flatbottomed potential. However, it has three options only: sphere, cylinder and layer. We wanted to create a combination of c

Re: [gmx-users] simulation_time

Original Message Subject: Re: simulation_time From:"Ms. Nikita Bora" Date:Mon, May 16, 2016 9:42 am To: nik...@tezu.ernet.in -- Respected Sir, Thanks for

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

ok thanks > Hi, > > Yes, that's one way to work around the problem. In some places, a module > subsystem can be used to take care of the selection automatically, but you > don't want to set one up for just you to use. > > Mark > > On Sun, May 15, 2016 at 11:48 AM wrote: > >> Thanks Mark, >> >> My

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

Please don't reply to entire digests. On 5/15/16 4:48 AM, Antara mazumdar wrote: Dear Justin, I am using the velocities from the NPT run. Could you please explain on the .cpt file you mentioned? This command: gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f MD.mdp -

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, Yes, that's one way to work around the problem. In some places, a module subsystem can be used to take care of the selection automatically, but you don't want to set one up for just you to use. Mark On Sun, May 15, 2016 at 11:48 AM wrote: > Thanks Mark, > > My sysadmins have let me install

Re: [gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

You can convert xpm2txt and plot in Origin as well Sent from my iPhone > On 29-Jan-2014, at 11:21 am, tarak karmakar wrote: > > Hi Monoj, > > You can use GNU 3D plot for this particular case. > > cheers, > Tarak > > > On Wed, Jan 29, 2014 at 8:02 AM, Monoj Mon Kalita > wrote: > >> Dear Gr

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Thanks Mark, My sysadmins have let me install my own GROMACS versions and have not informed me of any such mechanism. Would you suggest I qrsh into a node of each type and build an mdrun-only version on each? I'd then select a particular node type for a submit script with the relevant mdrun. Many

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55

Dear Justin, I am using the velocities from the NPT run. Could you please explain on the .cpt file you mentioned? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 --

Re: [gmx-users] PCA and FEL

Allright Sir Thank you very much for clearing the point. With Regards Suniba Sent from my iPhone > On 15-May-2016, at 12:14 pm, Tsjerk Wassenaar wrote: > > Hi Suniba, > > No, you will get the stability of configuration in the order parameters you > choose. But you don't know how much conforma