Re: [gmx-users] demo

allIs anyone using packmol to generate lipid bilayers ?http://www.ime.unicamp.br/~martinez/packmol/if yes, please let me know if anyone has faced any problems in using it to generate lipid bilayers. thanksanirbanuniv. of calgary ___ gmx-users mailing list

Re: [gmx-users] External Forces

toma0052 wrote: Hello, I am simulating a DPPC lipid bi-layer, and I would like to add an external force to, for example, one layer of the bilayer. Do I add an external force by specifying groups and the acceleration on those groups in the mdp file? Is there another way to do this? Do I ne

[gmx-users] demo

Original Message Date: Fri, 6 Oct 2006 11:29:58 +0530 (IST) From: sharada <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] From: A sharada Devi <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Sent Date: Thu 05 October 2006 [6:2:41 PM] Subject: Unable to run gromacs demo Gro

Re: [gmx-users] creating topology files

Owen, Michael wrote: Fellow gmx users, I am trying to create a topology file for TFE using the olpsaa/l force field to simulate a peptide in a mixed solvent. I created a molecule.itp file (as it was suggested in the manual), a molecule.gro file for TFE and I was able to place the several TF

Re: [gmx-users] g_rms, least square fit

kanin wichapong wrote: Dear All, I have some questions about g_rms. When I start to calculate the rmsd using g_rms first I will get "Select group for least squares fit" and then "Select group for RMSD calculation", does both two times need to be the same group or not? You can fit bas

Re: [gmx-users] Error with mdrun

[EMAIL PROTECTED] wrote: Hi, I am trying to run a lipid bilayer simulation, and everything seems to be fine until I try to run mdrun. The simulation stops immediately after I begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am not really sure what this error is, nor

Re: [gmx-users] pca on amber MD output

[EMAIL PROTECTED] wrote: Hi gromacs users, I am a new user to gromacs and realise that there are lots of comments on the archive already about using gromacs with amber outputs but I am getting rather mixed messages. I would like to clarify a few things. I have an Amber trjectory file saved thr

RE: [gmx-users] Error with mdrun

> I am trying to run a lipid bilayer simulation, and > everything seems to > be fine until I try to run mdrun. The simulation stops > immediately after I > begin mdrun, and I receive the error; p4_error: interrupt > SIGSEV: 11. I am > not really sure what this error is, nor what I should

RE: [gmx-users] GROMACS Parallel Runs

> I have successfully run gmx on up to 128 cpus. When I scale > to 256 cpus, the > following error occurs. Does it mean that gmx can't be run on > 256 nodes? > > Fatal error: > could not find a grid spacing with nx and ny divisible by the > number of > nodes (256) Isn't that just due to the

[gmx-users] g_rms, least square fit

Dear All,   I have some questions about g_rms. When I start to calculate the rmsd using g_rms first I will get "Select group for least squares fit" and then "Select group for RMSD calculation", does both two times need to be the same group or not? Like in my case, I want to calculate rmsd of on

Re: [gmx-users] RE: shake block problem

Jianhui Tian wrote: Hi GMX-Users, Does anyone have any idea about the problem? Thanks a lot in advance. I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _ splitting top

[gmx-users] RE: shake block problem

Hi GMX-Users, Does anyone have any idea about the problem? Thanks a lot in advance. I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _ splitting topology... Walking down

Re: [gmx-users] pca on amber MD output

Hi, Thank you for your advise. I am aware of the IED webpage and that's what drew my attention to the Angstrom, nm issue! However I had run pca without any conversion and my structure didn't get distorted, all analysis returns structures in Angstrom that don't appear out of place but what I a

[gmx-users] creating topology files

Title: creating topology files Fellow gmx users, I am trying to create a topology file for TFE using the olpsaa/l force field to simulate a peptide in a mixed solvent.   I created a molecule.itp file (as it was suggested in the manual), a molecule.gro file for TFE and I was able to place the

[gmx-users] External Forces

Hello, I am simulating a DPPC lipid bi-layer, and I would like to add an external force to, for example, one layer of the bilayer. Do I add an external force by specifying groups and the acceleration on those groups in the mdp file? Is there another way to do this? Do I need to alter any ot

Re: [gmx-users] pca on amber MD output

On Thursday 05 October 2006 16:56, [EMAIL PROTECTED] wrote: > Hi gromacs users, > > I am a new user to gromacs and realise that there are lots of comments on > the archive already about using gromacs with amber outputs but I am getting > rather mixed messages. > > I would like to clarify a few thin

[gmx-users] pca on amber MD output

Hi gromacs users, I am a new user to gromacs and realise that there are lots of comments on the archive already about using gromacs with amber outputs but I am getting rather mixed messages. I would like to clarify a few things. I have an Amber trjectory file saved through VMD in a .pdb format

[gmx-users] g_confrms_d options

Hi David,thanks again for the explanation. it makes a lot of sense now. any particular reference/s comes to your mind one should go thru regarding the same topic. it would really be a greta help. and thanks again. Arindam Ganguly ___ gmx-users mailing lis

[gmx-users] Range checking error: ci barely out of bounds.

Hello, I previously posted a problem about crashes in parallel but not serial: http://www.gromacs.org/pipermail/gmx-users/2006-September/024003.html I resolved that problem by running 5ns in serial and then, once I no longer needed to restrain the crystal waters, adding them to the main TIP4P

Re: [gmx-users] GROMACS Parallel Runs

Hi all, I have successfully run gmx on up to 128 cpus. When I scale to 256 cpus, the following error occurs. Does it mean that gmx can't be run on 256 nodes? Fatal error: could not find a grid spacing with nx and ny divisible by the number of nodes (256) Cheers, Sunny From: "Sunny" <[EMA

[gmx-users] Error with mdrun

Hi, I am trying to run a lipid bilayer simulation, and everything seems to be fine until I try to run mdrun. The simulation stops immediately after I begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am not really sure what this error is, nor what I should do to try to

Re: [gmx-users] g_confrms_d options

Arindam Ganguly wrote: Hi David, Thanks for the reply. very well i agree with what you have to say. however in that case the answer which i am getting for other options claiming that the lsq fit say for backbone is 0.98732 so on ., are useless values. now again if that is the case shoukld i a

[gmx-users] g_confrms_d options

Hi David,Thanks for the reply. very well i agree with what you have to say. however in that case the answer  which i am getting for other options claiming that the lsq fit say for backbone is 0.98732 so on ., are useless values. now again if that is the case shoukld i assume that native structure R

Re: [gmx-users] g_confrms_d options

Arindam Ganguly wrote: Hi Gmx-users, i am facing this problem i really don;t get it. i am trying to compare the rmsd of two strucures and when i use g_confrms_ d i the following options for the two structures Group 0 ( System) has 4276 elements Group 1 ( Protein) ha

[gmx-users] g_confrms_d options

Hi Gmx-users,i am facing this problem i really don;t get it. i am trying to  compare the  rmsd  of  two strucures  and when i  use  g_confrms_ d i  the following  options for the two structures Group     0 (      System) has  4276 elements Group     1 (     Protein) has  4276 elements