[gmx-users] How to fix Water during simulation ?

Hello Everyone, I am new in Gromacs. I am using gromacs for protein-ligand complex. I have few question ? 1): how to fix water during simulation ? 2): how to fix protein and ligand during simulation ? 3) how to fix few crystal water molecule during simulation ? 4) how to fix specific water

[gmx-users] Regarding NVT NPT ensemble

Dear Sir, I am new user in Gromacs. I am using Gromacs for protein-ligand complex. If I am not wrong MD simulation have three part. 1. Energy Minimization 2. Equilibration phase 3. Production phase After EM minimization we run Equilibration using (NVT NPT ensemble). I have little sily

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 52

+1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Regarding NVT NPT ensemble To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f0c4924.5020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/01/2012 1:14 AM, ajani

[gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

Respected Sir, Myself Haresh Ajani from National Institute of Pharmaceutical Education Research. I am using gromacs version 4.5.3. I am working on molded Protein. I am facing one problem in gromacs after minimization of the protein. I have put my query here. Fatal Error :

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Ajani haresh requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Ajani Accept invitation from Ajani haresh http://www.linkedin.com/e

[gmx-users] Hw to use the G_anaeig.................?

me I hope any one I will get better response. -- Ajani Haresh NIPER-IICB KOLKATA 9836182127 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] how to find conformational free energy?

know plz help me. thanks... -- Ajani Haresh NIPER-IICB KOLKATA 9836182127 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

[gmx-users] How to find Enthalpy And Entropy ?

and entropy from this file. any one know plz help me... -- Ajani Haresh NIPER-IICB KOLKATA 9836182127 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http