Re: [gmx-users] prodrg and charge groups

Diane, I can't speak to charge groups, but in terms of charges, I think I remember that prodrg has a number of disclaimers about its charges. Personally, I would be rather reluctant to use prodrg charges for simulating ligands. A fast alternative would be to download the Antechamber package, whic

[gmx-users] prodrg and charge groups

Title: prodrg and charge groups I don't know if this has already been discussed, but I'm wondering how the charges and charge groups are assigned by PRODRG. I'm curious about this because I have been using it for a few similar ligands which all contain a steroid (estradiol) moiety. In the thr

[gmx-users] g_hbond -g

Hi list, I couldn't find in the archives and "3.2 to 3.3 changes" what happened to "-g" flag in g_hbond ? Is the old "hbond.log" information written somewhere else ? Diego Enry. // command line g_hbond_331i -g(intel compiled) // error message: Program g_hbond_331i, VERSION 3.3.1 Source cod

Re: [gmx-users] Re: Re; Force Calculation

Hi, On Jun 29, 2006, at 4:41 PM, Justin M. Shorb wrote: Erik and Mark: Thanks for your help, I will begin diving into the code today. Mark, if everything went ideally (which things don't always), I would use the force tables to compute the total SR electrostatic force on each atom in a s

[gmx-users] Re: Re; Force Calculation

Erik and Mark: Thanks for your help, I will begin diving into the code today. Mark, if everything went ideally (which things don't always), I would use the force tables to compute the total SR electrostatic force on each atom in a specific group (around 2 to 7 atoms). The same goal can be acc

Re: [gmx-users] Analysing using InsighII Decipher

raja wrote: Dear All, Any strategy available for analyzing gromacs trajectory in insightII, Decipher module. Kindly let me know. Please start with doing your own homework... what formats does that module read? What formats can gromacs write? What sorts of analysis do you want to do? Are there

[gmx-users] Analysing using InsighII Decipher

Dear All, Any strategy available for analyzing gromacs trajectory in insightII, Decipher module. Kindly let me know. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Choose from over 50 domains or use your own ___ gmx-

Re: [gmx-users] Supradiffusivity

2006/6/28, 이 선주 <[EMAIL PROTECTED]>: Hello UsersI have seen that it is needed to define three separate groups forcenter-of-mass motion removal: water and a separate group for each lipid layer in order to remove supradiffusivity of the two leaflets.Can anyone tell me whether my settings are correct

[gmx-users] Using tpbconv

Hi I have always used tpbconv to do my restarts however after reading the newer documentation, I have noticed that it only mentions that the energy file can be used with Pressure Coupling or Noose Hoover temperature coupling, so what is the correct usage when using berendsen temperature coupli

Re: [gmx-users] Can a Serial MD simulation be continued in, Parallel?

Sridhar Acharya wrote: Hi, But will that not do a new simulation rather than an exact continuation of the previous simulation? Only if you tell it to As it says in the documentation (for example, man grompp), you can supply the magic information for continuing simulations from the .edr

Re: Re: [gmx-users] Can a Serial MD simulation be continued in, Parallel?

Hi, But will that not do a new simulation rather than an exact continuation of the previous simulation? sridhar -- Message: 4 Date: Thu, 29 Jun 2006 18:48:45 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Can a Serial MD simulation be cont

Re: [gmx-users] How do Charge Groups work?

From: "X.Periole" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] How do Charge Groups work? Date: Wed, 28 Jun 2006 20:29:17 +0200 I had a system where I have no charges in it, but I do have Lennard-Jones non-bo

RE: [gmx-users] How do Charge Groups work?

Title: RE: [gmx-users] How do Charge Groups work? -Original Message- From: [EMAIL PROTECTED] on behalf of X.Periole Sent: Wed 6/28/2006 7:29 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How do Charge Groups work? >> I had a system where I have no charges in it

Re: [gmx-users] Can a Serial MD simulation be continued in Parallel?

Sridhar Acharya wrote: Dear GMX-users I want to know whether a MD simulation that was run as a serial job could be continued in parallel using tpbconv? If so, how to give the number of processors for the command? There's no reason you couldn't use grompp with the .trr and .edr files as inpu

Re: [gmx-users] Force Calculation

Hi, Where I've gotten is to: /src/gmxlib/nonbonded/nonbonded.c which calls the machine specific kernels. I am more than willing to work through this myself, but can anybody point me to a good book/site that explains what is actually going on when Gromacs looks up these forces? Try r

[gmx-users] Can a Serial MD simulation be continued in Parallel?

Dear GMX-users I want to know whether a MD simulation that was run as a serial job could be continued in parallel using tpbconv? If so, how to give the number of processors for the command? Regards, sridhar -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandi