Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 14

command? Is > there any other option to capture the water mediated Hbonds? Please > suggest something. > Sunipa Sarkar > > > -- > > Message: 3 > Date: Tue, 7 May 2019 09:14:42 +0200 > From: Mark Abraham > To: Discussion list for GROMACS use

[gmx-users] GROMOS 54A8 Force field

Dear users, Could you please suggest me where I can get the complete package of GROMOS 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker ( https://pubs.acs.org/doi/10.1021/ct300156h). Looking forward to your suggestions. Thanks in advance. Sincerely yours, Kalyanashis Jana

[gmx-users] REMD analysis

forward to hear from you. Thanks in advance, Kalyanashis Jana -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Temperature interval in REMD simulations

limit and exchange probability is enough to produce reasonable results? Thanks in advance, Kalyanashis Jana On Thu, Nov 17, 2016 at 6:11 PM, Kalyanashis Jana <kalyan.chem...@gmail.com> wrote: > Dear gromacs user, > I am trying to do REMD simulation for protein having 8320 atoms (including >

Re: [gmx-users] Replica Exchange MD

Thank you very much for your reply and suggestions. I am discussing with system admin regarding this issue. With Best Regards, Kalyanashis Jana On Wed, Oct 5, 2016 at 6:01 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Wed, Oct 5, 2016 at 2:17 PM Kalyanashis Ja

Re: [gmx-users] Replica Exchange MD

user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 With Best Regards, Kalyanashis Jana On

[gmx-users] Replica Exchange MD

D run when the simulations have been run individually using "mpirun -np 10 mdrun_mpi -v -s topol.tpr " Please suggest me, how can I overcome this problem. Looking forward to hear from you. Thanks in advance, Kalyanashis Jana -- Thanks with regards Kalyanashis Jana -- Gromacs Users ma

[gmx-users] genbox command in gromacs-5.0.1

tools. In gromacs site, it is written that genbox This tool has been split to gmx solvate and gmx insert-molecules. Can anyone please help me? Thanks in advance, Kalyanashis Jana -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive

[gmx-users] MD run failed..

= 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanks in advance, Kalyanashis Jana. -- Kalyanashis Jana email: kalyan.chem

[gmx-users] Energy minimization of an UNKNOWN molecule.

? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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 http://www.gromacs.org/Support

Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

.. On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem

Re: [gmx-users] Energy minimization of an UNKNOWN molecule.

order for directive atomtypes Please help me.. On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File

Re: [gmx-users] Erro in SMD simulation..

Thank you Justin so much... In case of this system rectangular (10x10x25) is working.. SMD is over with out any error.. Thank you.. On Wed, Apr 2, 2014 at 12:03 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5015557...@n6.nabble.com wrote: On 4/1/14, 2:18 PM, Kalyanashis wrote: Thank you

Re: [gmx-users] Erro in SMD simulation..

fine? Thanks, Kalyan. On Tue, Apr 1, 2014 at 7:06 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5015544...@n6.nabble.com wrote: On 4/1/14, 6:16 AM, Kalyanashis wrote: Dear all, I am trying to run an SMD simulation of an enzyme system with a drug molecule. The final SMD run

Re: [gmx-users] Erro in SMD simulation..

Thank you so much Justin. Now I am trying with a rectangular box. I don not whether it will work or not. On Tue, Apr 1, 2014 at 10:51 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5015553...@n6.nabble.com wrote: On 4/1/14, 12:56 PM, Kalyanashis wrote: Thank you Justin for your valuable

[gmx-users] Error in MD Simulation...

I have submitted a job for PR MD simulation but I got an error Program mdrun, VERSION 4.6.3 Source code file: /compile/gromacs-4.6.3/src/gmxlib/checkpoint.c, line: 1619 File input/output error: Cannot rename checkpoint file; maybe you are out of disk space? For more information and tips for