[gmx-users] Fw: ionic liquids

-- Original Message -- From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org

Re: [gmx-users] Fw: ionic liquids

On 4/30/2011 5:20 PM, Prema Awati wrote: */-- Original Message --/* From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org Date: Sat, 30 Apr 2011 10:30:53 +0530 (GMT+05:30) Subject: ionic liquids Sir, I am trying to create an ionic-liquid system comprising of

Re: [gmx-users] sulfate ion

On 4/30/2011 3:54 PM, saly jackson wrote: Hi all I want to know about the ability of GROMACS to simulate sulfate in(SO4 (2-)), Do we can have the ion in our simulation using GROMACS? You asked this question on Wednesday, and got an answer. Googling sulfate gromacs finds that answer. If you

Re: [gmx-users] Gromacs 4.5.4 MPI

On 4/30/2011 8:50 AM, Juliette N. wrote: Dear experts, I have successfully installed a normal gromacs 4.5.4 installation on one of my machines. I have read the Installation Instructions that As of GROMACS 4.5, threading is supported, so for e.g multi-core workstations, MPI is no longer

Re: [gmx-users] LINCS error- 4.5.4 installation?

On 4/30/2011 9:06 AM, Juliette N. wrote: Dear experts, I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps I get LINCS error: step 400, will finish Sat Apr 30 05:20:45 2011 Step 750, time 1.5 (ps) LINCS WARNING relative constraint deviation after LINCS: rms

Re: [gmx-users] Re: Tcoupl default setting

On 4/30/2011 4:47 AM, Charlie Forde wrote: Thank you Mark for your response, In carrying out the test you recommended I realised that I had set the integrator to sd, in such a case the tcoupl parameter is ignored. This explains my well behave temperature in the absence of setting a tcoupl

[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

×M5~Ë­­ªyïxã]¹ß]7ãMuÓ Program mdrun, VERSION 4.0.7Source code file: checkpoint.c, line: 565Fatal error:Attempting to read a checkpoint file of version 12 with code of version 4-- 83_kargar-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be

Re: [gmx-users] rigid tetrahedral molecule

On 2011-04-30 00.38, Mark Abraham wrote: On 4/30/2011 5:05 AM, Sanku M wrote: Hi David, Actually, I had tried to use vsites to make this molecule rigid. I read the manual section 4.7 as well. But, unfortunately, for a 5-site tetrahedral geometry I was not able to figure out the right vsite type

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

On 4/30/2011 7:22 PM, Faezeh Kargar wrote: Dear gmx users, My code stops running because of electricity voltage oscillation. it happened for several times and each time I restarted running my code. but for this time with command mdrun -s topol.tpr -x

[gmx-users] Simulations in vacuo - energy increase

Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure

Re: [gmx-users] Simulations in vacuo - energy increase

On 2011-04-30 14.17, Zoe Hall wrote: Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of

[gmx-users] Alkanes, Alkens in Amber forcefield

Hi all I need .itp and .mdp files of some Alkanes such as Hepane, Decane and Heptene, Decene in Amber forcefield. Would you please help me? Best Regards Thanks alot Maria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

htmldiv On 4/30/2011 7:22 PM, Faezeh Kargar wrote: Dear gmx users, My code stops running because of electricity voltage oscillation. it happened for several times and each time I restarted running my code. but for this time with command mdrun -s topol.tpr -x

[gmx-users] Re: ionic liquids

I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of

Re: [gmx-users] Alkanes, Alkens in Amber forcefield

Maria Hamilton wrote: Hi all I need .itp and .mdp files of some Alkanes such as Hepane, Decane and Heptene, Decene in Amber forcefield. Would you please help me? Such species should be trivial to generate using antechamber (with GAFF, perhaps). There are various scripts to convert

Re: [gmx-users] Re: ionic liquids

If you are sure about the force field (the one from Lopes et al.?) you are using, build a dilute system, and then run long enough simulations using NTP ensemble. possibly using simulation annealing. ? 2011-4-30 16:44, Vitaly Chaban ??: I am trying to create an ionic-liquid system

[gmx-users] lyzosyme tutorial

Dear Justin   I have started lyzosyme tutorial. when using the command pdb2gmx I get the following error. Please guide me to solve it thanks Regards D. Aghaie    Program pdb2gmx, VERSION 4.0.99-dev-20100315 Source code file: /apps/gromacs/build/gromacs-4.5-beta3/src/kernel/pdb2top.c, line: 147

[gmx-users] How to use Inflategro with different lipid types

Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The