[gmx-users] Viscosity calculations

2011-01-16 Thread Xiaohu Li
Hi, I'm trying to calculate viscosities of a few ionic liquid and has roughly read about Hess's paper JCP 116 209, 2002. Follows are the questions that I have (1) For the method which uses the fluctuations of the pressure tensor using Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis o

[gmx-users] ACPYPE

2011-01-16 Thread Kerrigan, John
Go to http://code.google.com/p/acpype/wiki/HowToUse for instructions on installation of ACPYPE. There are also some very nice acpype tutorials located at http://code.google.com/p/acpype/w/list Enjoy! John John E. Kerrigan, Ph.D. Associate Director Bioinformatics The Cancer Institute o

Re: [gmx-users] ACPYPE download

2011-01-16 Thread Mark Abraham
On 17/01/2011 5:05 AM, Jianhui Tian wrote: Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone wh

Re: [gmx-users] Position restraint problem

2011-01-16 Thread Mark Abraham
On 17/01/2011 6:25 AM, Marcelo Silva wrote: Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the

Re: [gmx-users] Position restraint problem

2011-01-16 Thread Justin A. Lemkul
Marcelo Silva wrote: Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tr

[gmx-users] Position restraint problem

2011-01-16 Thread Marcelo Silva
Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tried to restrain the posi

[gmx-users] ACPYPE download

2011-01-16 Thread Jianhui Tian
Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone who has successful experience using ACPYPE and wou

Re: [gmx-users] problem with LINCS

2011-01-16 Thread Justin A. Lemkul
Thomas Koller wrote: Hello! I have the following problem: I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equ

[gmx-users] problem with LINCS

2011-01-16 Thread Thomas Koller
Hello! I have the following problem: I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equilibration. A few steps a

Re: [gmx-users] grompp error

2011-01-16 Thread Mark Abraham
On 16/01/2011 7:09 PM, bharat gupta wrote: Hi I am using gromacs 4.5.3 ... I am using OPLSS force field in simulation and while issuing grompp command for energy minimzation I am getting an error "No molecule type NA+ exists" ... I used NA+ while issuing genion command ..., can anybody tell me

Re: [gmx-users] segmentation error

2011-01-16 Thread Mark Abraham
On 16/01/2011 8:43 PM, leila separdar wrote: I managed to run my simulation but which kind of coulomtype can I use except PME? Do you have charges? If so, follow standard practice in the literature for treating them. also I get different averages for kinetic and potential energies than bef

Re: [gmx-users] Installing Gromacs with Cygwin

2011-01-16 Thread Mark Abraham
On 16/01/2011 9:27 PM, Mr Bernard Ramos wrote: Dear all, I need help. I am trying to install Gromacs using Cygwin. However, I do not seem to have access to it. I am very new with Cygwin. I just followed the steps provided by the following sites: http://machine-phase.blogspot.com/2009/04/how-

[gmx-users] Installing Gromacs with Cygwin

2011-01-16 Thread Mr Bernard Ramos
Dear all, I need help. I am trying to install Gromacs using Cygwin. However, I do not seem to have access to it. I am very new with Cygwin. I just followed the steps provided by the following sites:  http://machine-phase.blogspot.com/2009/04/how-to-install-gromacs-on-windows-vista.html and http:

[gmx-users] segmentation error

2011-01-16 Thread leila separdar
I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about

[gmx-users] grompp error

2011-01-16 Thread bharat gupta
Hi I am using gromacs 4.5.3 ... I am using OPLSS force field in simulation and while issuing grompp command for energy minimzation I am getting an error "No molecule type NA+ exists" ... I used NA+ while issuing genion command ..., can anybody tell me where am I going wrong?? -- Bharat Ph.D. Can