[gmx-users] [Fwd: Oueries]

Original Message Subject:Oueries Date: Mon, 10 Sep 2007 08:08:40 +0100 (BST) From: Moutusi Manna <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Hi, I have started using GROMACS recently. As per information GROMACS is the fasted MD pacage . But, when I perform

Re: [gmx-users] [Fwd: Oueries]

Try running mdrun with -nice 0. Regards, Yang Ye - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, September 10, 2007 3:31:35 PM Subject: [gmx-users] [Fwd: Oueries] Original Message Subject: Ou

Re: [gmx-users] [Fwd: Oueries]

David van der Spoel wrote: Original Message Subject: Oueries Date: Mon, 10 Sep 2007 08:08:40 +0100 (BST) From: Moutusi Manna <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Hi, I have started using GROMACS recently. As per information GROMACS is the fasted MD

Re: [gmx-users] [Fwd: Oueries]

maybe you could set the nicelevel to a higher priority David van der Spoel a écrit : Original Message Subject: Oueries Date: Mon, 10 Sep 2007 08:08:40 +0100 (BST) From: Moutusi Manna <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Hi, I have started usi

Re: [gmx-users] Partial Charge Units in GROMACS.

yes. On 9/10/2007 9:34 AM, Travis Trudeau wrote: My apologies if this question is rather elementary, but we are uncertain what the units of partial charge are in GROMACS (i.e. in library files like ffG43a1.rtp) - we are assuming they are units of elementary charge ( i.e. charge of one electron

Re: [gmx-users] make_edi command options

Anirban, Exactly what it says in the manual: the indices of eigenvectors to include; a string consisting of one or more numeric characters if needed separated by spaces... Tsjerk On 9/10/07, Anirban Ghosh <[EMAIL PROTECTED]> wrote: > Hi All, > I want to use the make_edi command in GROMACS for cr

[gmx-users] make_edi command options

Hi All, I want to use the make_edi command in GROMACS for creating the .edi file for analysing some eigenvectors. For using the make_edi command there is an option of selecting the algorithm (-linfix / -linacc / rdfix) with "string" value. I shall be glad if someone can tell me what value has to

[gmx-users] Generating a solvent box

Hello gmx users, I have a query to ask.It would be nice if someone could suggest me on this.I have a tfe molecule generated using InsightII program package.Now I would like to create a box containing a fixed number of tfe molecules based on its density.I tried using "genbox" and "ge

Re: [gmx-users] Generating a solvent box

Quoting Dilraj Lama <[EMAIL PROTECTED]>: > Hello gmx users, > I have a query to ask.It would be nice if someone could > suggest me on this.I have a tfe molecule generated using > InsightII program package.Now I would like to create a box > containing a fixed number of tfe molecules

Re: [gmx-users] Generating a solvent box

Hello justin, Here is what I did.I initially defined a cubic box into which I placed the TFE molecule.This I did using editconf.Then I used genconf with the follwing command. genconf_mpi -f tfe-box-four.gro -o out-four.pdb -nbox 5 5 5 Yes I am able to generate a regular arrangment o

Re: [gmx-users] Generating a solvent box

Dilraj Lama wrote: Hello justin, Here is what I did.I initially defined a cubic box into which I placed the TFE molecule.This I did using editconf.Then I used genconf with the follwing command. genconf_mpi -f tfe-box-four.gro -o out-four.pdb -nbox 5 5 5 Yes I am able to generate a

RE: [gmx-users] Adding two peptides in a water box

Hi Guys, Thank very much for your time trying to help me with this issue. It seems from all your answers that adding two identical peptides, separated by a certain distance from each other, and then put them into a water box with ions is a simple task. However, it is still puzzling me. Altho

[gmx-users] "check14" and "shuffle" options in grompp command

Hey, Everyone, Question about options for grompp command: (1) "check14": the description is "Remove 1-4 interactions without Van der Waals". What's the meaning by "Van der Waals"? Does it mean if there is no corresponding Van der Waals parameter defined in [ pairtypes ], the item in [ pairs ] w

Re: [gmx-users] frozen group, pull code and COM motion removal

In message <[EMAIL PROTECTED]> (on 9 September 2007 19:35:32 +0200), [EMAIL PROTECTED] (David van der Spoel) wrote: >[someone] wrote: >> Hi all, >> >> Recently, I performed a simulation which have three groups: frozen group >> (there's no connections with the other groups), free group (peptide),

Re: [gmx-users] "check14" and "shuffle" options in grompp command

On 9/11/2007 7:05 AM, WU Yanbin wrote: Hey, Everyone, Question about options for grompp command: (1) "check14": the description is "Remove 1-4 interactions without Van der Waals". What's the meaning by "Van der Waals"? Does it mean if there is no corresponding Van der Waals parameter define

[gmx-users] Change in distances between two atom during MD

Hi all, I want to get the plot of Change in distances between two atom during MD simulation. what program can I use? Thank you in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please searc

Re: [gmx-users] Change in distances between two atom during MD

Rui Li wrote: Hi all, I want to get the plot of Change in distances between two atom during MD simulation. what program can I use? Manual section 7.4 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

Re: [gmx-users] "check14" and "shuffle" options in grompp command

Yang Ye wrote: On 9/11/2007 7:05 AM, WU Yanbin wrote: Hey, Everyone, Question about options for grompp command: (1) "check14": the description is "Remove 1-4 interactions without Van der Waals". What's the meaning by "Van der Waals"? Does it mean if there is no corresponding Van der Waals

[gmx-users] Exclusions for aromatic residues

Hi, In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example), exclusions seem to be listed only for aromatic residues such as TYR, HIS, and TRP. Why is that so? Sanghwa Han ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

Re: [gmx-users] Exclusions for aromatic residues

한상화 wrote: Hi, In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example), exclusions seem to be listed only for aromatic residues such as TYR, HIS, and TRP. Why is that so? normally they are generated (chapter 4) but one can define extra exclusions. interactions within rings usualy