Re: [gmx-users] make_ndx

Hello, Manuel, Thank you very much for your trick. It is neat. Have a nice weekend! Dongsheng On Sun, 2006-06-25 at 02:58 +0200, Manuel Prinz wrote: > Hello Dongsheng! > > Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang: > > In make_ndx, I would like to keep two groups, for in

Re: [gmx-users] make_ndx

Hello Dongsheng! Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang: > In make_ndx, I would like to keep two groups, for instance, group 4 and > group 5. I have try it in two ways, namely, "keep 4 & keep 5" and "keep > 4 | keep 5". However both ways only keep group 4. Anyway to accom

[gmx-users] make_ndx

Hello, gmx users: In make_ndx, I would like to keep two groups, for instance, group 4 and group 5. I have try it in two ways, namely, "keep 4 & keep 5" and "keep 4 | keep 5". However both ways only keep group 4. Anyway to accomplish my task is to delete other groups one by one, but it is not so c

Re: [gmx-users] energy minimization

Hi, David, Thank you for your help. I have fix it now. Have a nice weekend! Dongsheng On Sat, 2006-06-24 at 21:53 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Hello, everyone, > > > > I have a system with a nanotube and a polymer chain. First I did EM for > > the system in v

Re: [gmx-users] energy minimization

Dongsheng Zhang wrote: Hello, everyone, I have a system with a nanotube and a polymer chain. First I did EM for the system in vacuum. After that, I added some water to my system, and tried to do EM again. This time I got some large force on some atoms. The messages are as folllows: Step=0,

[gmx-users] energy minimization

Hello, everyone, I have a system with a nanotube and a polymer chain. First I did EM for the system in vacuum. After that, I added some water to my system, and tried to do EM again. This time I got some large force on some atoms. The messages are as folllows: Step=0, Dmax= 5.0e-03 nm, Epot= -

Re: [gmx-users] Energy of part of system

Beniamino Sciacca wrote: I use interaction energy to estimate the interaction forces between the molecules When the course of Potential (or DNA1-DNA2...) is constant, I use these values for estimate interaction forces. So I'm using equilibrium value, isn't it? My comment was half-joki

Re: [gmx-users] electostatic

mahbubeh zarrabi wrote: Dear freinds can i study electrostatic interactions in complex by gromacs? how?whould you please help me? your question is too vague. thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection arou

[gmx-users] electostatic

Dear freinds can i study electrostatic interactions in complex by gromacs? how?whould you please help me? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___

Re: [gmx-users] errors on carbon nanotube

[EMAIL PROTECTED] wrote: Hi,GMX group and other users: I am a gromacs(version 3.3) user. I want to do carbon nanotube(CNT) MD. Months ago, when I ran grompp, she told me that something was wrong. (see http://www.gromacs.org/pipermail/gmx-users/2006-April/021092.html) After i got suggestions from

Re: [gmx-users] Energy of part of system

I use interaction energy to estimate the interaction forces between the molecules When the course of Potential (or DNA1-DNA2...) is constant, I use these values for estimate interaction forces. So I'm using equilibrium value, isn't it? What can I do? is the file pull.pdo the only other w