Re: [gmx-users] Using h-angles taking to much time

harpreet singh wrote: Dear Sir, I am running Molecular dynamics simulation. Using other constraints the program is running very fast but if I am using constraints = h-angles or all-angles the program is taking too much of time (running since last 12 hours). Kindly suggest me that is it th

[gmx-users] Using h-angles taking to much time

Dear Sir, I am running Molecular dynamics simulation. Using other constraints the program is running very fast but if I am using constraints = h-angles or all-angles the program is taking too much of time (running since last 12 hours). Kindly suggest me that is it the normal behavior of the pr

Re: [gmx-users] applying force and fixing atoms in gromacs

Ah, groovy, I was clearly using the wrong search terms, and didn't make the connection when I was looking through the contents. Cheers -Adam On 10/19/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Adam Fraser wrote: > > Hello, > > > > I was looking in the manual for how to fix atoms and apply co

Re: [gmx-users] Pull code with runtype start

dtmirij wrote: Hello everyone, I just want to clarify if the runtype "start" option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. Did you try searching the manual for "runtype"? Mark ___ gmx-users mai

Re: [gmx-users] applying force and fixing atoms in gromacs

Adam Fraser wrote: Hello, I was looking in the manual for how to fix atoms and apply constant (or time dependent) force to atoms. Could someone please help me get started with this? Curiously enough, the manual is the place to start. Look for freeze groups and AFM pulling. Mark _

[gmx-users] Pull code with runtype start

Hello everyone, I just want to clarify if the runtype "start" option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. If I have runtype = start in my pull.ppa file then gromacs gives me an error:

[gmx-users] applying force and fixing atoms in gromacs

Hello, I was looking in the manual for how to fix atoms and apply constant (or time dependent) force to atoms. Could someone please help me get started with this? Thank you, Adam ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.or

RE: [gmx-users] 1-4 table size of 0 nm

From: "Adrien Leygue" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: [gmx-users] 1-4 table size of 0 nm Date: Fri, 19 Oct 2007 14:47:27 +0300 Dear Gromacs users, I am using Gromacs with a fully tabulated potentials. I have crea

[gmx-users] 1-4 table size of 0 nm

Dear Gromacs users, I am using Gromacs with a fully tabulated potentials. I have created the table_X_Y.xvg and tablep_X_Y.xvg files (which are identical in my case) but when I run gromacs to perform an initial energy minimization I get the following error message: Warning: 1-4 interaction betwe

RE: [gmx-users] qasi-harmonic entropy calculation

Hi Pedro, I am using 4565.9 as a conversion factor. I dont see any problem unless any condtion I needed to satisfy during the simulation. Simulation gave the result what I had expected. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [E

Re: [gmx-users] uneven distribution of water across the bilayer

Dear Mark, Thanks a lot for your valuable time, and sorry for inappropriate description, I am describing again, I hope thin time I can make it clear. I took preequilibrated POPE.pdb files which already have SPC water molecules I had deleted these water molecules and change the box size at 'Z