[gmx-users] Umbrella Sampling

Hi everyone, I have run pulling simulation for the protein complex system. I have got 1000 configuration files. And in the summary_distances.dat, I have found 0-500 distances. How will I select configuration file for the npt_umbrella simulation. Thanks in advance. I will be very grateful for

[gmx-users] steered molecular dynamics

Hi, I would like to run steered molecular dynamics (SMD) in my protein complex system to find out the PMF without using umbrella sampling. In the tutorial:after equilibration, the steps are: (a) Generating Configurations: pull code are used, configurations files are generated, (b) umbrella

Re: [gmx-users] steered molecular dynamics

Hi Sir, Many thanks for the help. I would like to run steered molecular dynamics (SMD) in my protein complex system to find out the PMF without using umbrella sampling. In the tutorial: after equilibration, the steps are: (a) Generating Configurations: pull code are used, configurations files

[gmx-users] steered molecular dynamics

Hi everyone, I would like to run steered molecular dynamics (SMD) in my protein complex system. I have studied the tutorial of umbrella sampling in gromacs. Can anyone suggest me about SMD? Thanks in advance. Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Center of mass

Thanks Dr. Justin. Thank you for your generous support. On Wed, Oct 26, 2016 at 10:27 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/25/16 7:07 PM, Mouri Ahmed wrote: > >> Hi >> >> I have been looking at options for calculating center of m

[gmx-users] Center of mass

Hi I have been looking at options for calculating center of mass distance between two proteins. If anyone has worked with the center of mass in gromacs and have notes they could share I'd very grateful. Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] restraint

Dear Sir, Thanks for the quick response. Best Regards Mouri On Tue, Oct 25, 2016 at 9:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/25/16 6:11 AM, Mouri Ahmed wrote: > >> Dear Dr. Justin, >> >> Thank you very much for the help. >> >

Re: [gmx-users] restraint

edu> wrote: > > > On 10/25/16 5:24 AM, Mouri Ahmed wrote: > >> Hi >> >> I want to use distance restraint between protein and ligand in gromacs. >> >> I am confused with the problem. >> >> A

[gmx-users] restraint

Hi I want to use distance restraint between protein and ligand in gromacs. I am confused with the problem. Anyone have any ideas? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Restraint

Hi I want to use distance restraint between protein and ligand in gromacs. I am confused with the problem. Anyone have any ideas? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] distance restraint

Hi I want to use distance restraint between protein and ligand in gromacs. How could I use distance restraint? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] mdp

Thanks Mark I will check the force field. Best Regards Mouri On Tue, Oct 18, 2016 at 3:00 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > What does your background reading on applications of that force field > suggest to you? > > Mark > > On Tue,

Re: [gmx-users] mdp

Hi Thanks Justin and Parvez for your suggestions. Can I use "constraints=none" for coarse-grain protein also? Best Regards Mouri On Mon, Oct 17, 2016 at 8:53 AM, Justin Lemkul wrote: > > > On 10/16/16 2:16 PM, Parvez Mh wrote: > >> Hey; >> >> Go through the link

[gmx-users] mdp file

Hi I want to use no constraint in my MD simulation. What will I write in my mdp file? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] mdp

Hi I want to use no constraint in my MD simulation. What will I write in my mdp file? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read