[gmx-users] Please help

, With reagards Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing list

[gmx-users] DNA MD PROBLEM

Hello, This is Anik Sen from India. Am using Gromacs 4.5.5. to do some calculations on solvation and ligand binding interactions with DNA. I have some questions regarding the problem. As water is present in the system, so according to the manual the define in the .mdp file must

RE: [gmx-users] to know about constraints

-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, June 20, 2012 12:09 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 6/19/12 2:35 PM, Anik Sen wrote: Hello Justin, This is Anik again. I

RE: [gmx-users] to know about constraints

...@anu.edu.au] Sent: Wednesday, June 20, 2012 1:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 20/06/2012 5:24 PM, Anik Sen wrote: Hello Justin For freezefprs, am using the .mdp file as follows: ; title = NACL6 cpp

RE: [gmx-users] to know about constraints

Dear Mark, i GOT IT. I understood my mistake and now it is running. Thanx for your help. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Wednesday, June 20, 2012 2:50 PM To: Discussion

[gmx-users] to know about constraints

calculation. The water molecules and other atoms may be in movement during the calculation. Thanx in advance Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org

RE: [gmx-users] to know about constraints

] to know about constraints On 6/19/12 1:28 PM, Anik Sen wrote: Dear gromacs developers, This is Anik. For a certain work with nonbonded interactions with alkali halides and water, I need to constrain some specific atoms in the energy minimization step

RE: [gmx-users] to know about constraints

. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Tuesday, June 19, 2012 11:13 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] to know about constraints Thanx Justin. I will check the links

[gmx-users] hello

with the water molecules may not hamper but it may not dance so much in the solvation box. Thanx in advance Anik Sen. Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002

RE: [gmx-users] Regarding errors

Dear Suryanarayana Seera Please check the itp files mentioned in the topol.top and what u used in your commands. Especially check the solvent model. May be you have not changed that in the topol.top file. From: gmx-users-boun...@gromacs.org

[gmx-users] problem

Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. I was trying to run the dynamics for some inorganic metal halides solvation in water. A fatal error is comingthat: * Atomtype CH2r not found. But in my system I have no such atoms. Only water molecules with tip4p model

[gmx-users] Cut off problem

changed the ‘d’ and ‘rlist’; rvdw’ and rcoulomb’ to a number of different values to overcome the problem, but the problem persists. How can I overcome this problem. Thanking you in advance Anik Sen Anik Sen Student CSIR-Central Salt Marine

[gmx-users] To know

Hi, Am Anik Sen, using gromacs 3.3.2 version. I have a very simple question to ask, In the mdp file, like the emmod.mdp or run.mdp needed for a MD run there are three factors namely, rlist, rcoulomb and rvdw. 1. Is there any minimum value for these three below which the results

[gmx-users] (no subject)

number. 2. I have three different substrates. I want to create a same box size irrespective of the size of my molecule and generate same number of water molecules around them. What should I do? Thanking in advance. Anik Anik Sen

[gmx-users] A query

. Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing listgmx-users

RE: [gmx-users] A query

...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, January 31, 2012 7:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] A query On 31/01/2012 9:04 PM, Anik Sen wrote: Hello, Am anik. Am using gromacs 4.5.5 I could not find the proper reason

[gmx-users] (no subject)

. Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] A query

: Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms while sorting atoms. Thanks in advance Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002

[gmx-users] topology missing

? Thanking n advance Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing

[gmx-users] a query

what will be the residue files for DNA. Please suggest. Thanks in advance. Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org

RE: [gmx-users] a query

...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, January 24, 2012 3:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] a query On 24/01/2012 8:32 PM, Anik Sen wrote: Hello Anik here. I think its a silly question but, could not stop to ask as its between

RE: [gmx-users] (no subject)

] (no subject) Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems

RE: [gmx-users] (no subject)

El 11/01/12 12:07, Anik Sen escribió: I have already done that but the problem persisits. From: gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j

RE: [gmx-users] HEME topology

Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal

[gmx-users] (no subject)

Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] problem

What to do? Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing listgmx

[gmx-users] thanx

thanx justin for the help Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users