Re: [gmx-users] other output format of Matrix Data than xpm format

/* C proof e-mail --- Hi Florian, Sure. Here's an example for writing a matrix (real **mat) to an ascii file or as a .pgm grayscale file with 1 (up to 256 levels) or 2 bytes (up to 65536 levels). This file format is not very condensed, but is very easy to handle. To process in python, you could

[gmx-users] electrostatic and vdw energies from snapshots

hello, i would like to calculate the vdw and electrostatic energies for a part of my system that was not included in the energy groups during md. as a rerun would be too time consuming, i thought of taking snapshots from the md run, minimising those with the part of interest included in the

Re: [gmx-users] electrostatic and vdw energies from snapshots

hi tserjk, that sounds great. thanks a lot. merc Original-Nachricht Datum: Thu, 5 Apr 2007 11:44:04 +0200 Von: Tsjerk Wassenaar [EMAIL PROTECTED] An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] electrostatic and vdw energies from snapshots

Re: [gmx-users] electrostatic and vdw energies from snapshots

Hi Merc, Why not resample your trajectory with a lower time resolution (i.e. extracting snapshots) and only -rerun the resampled trajectory? Sounds less time consuming than minimizing a number of snapshots. Cheers, Tsjerk On 4/5/07, merc mertens [EMAIL PROTECTED] wrote: hello, i would like

[gmx-users] Re: electrostatic and vdw energies from snapshots

Maybe it is an obvious observation, but reruns are not as time consuming as original runs. If I'm not wrong, as snapshots are generally saved every 2500-1 time-steps, reruns are 2500-1 faster than original runs. So, maybe a simple rerun with new 'energygrps' is your option.

Re: [gmx-users] Prot_prep_problem

pkmukher wrote: Hello group users, I am trying to prepare a protein using the pdb2gmx module of gromacs.I have stripped the hydrogens using a different program and using a pdb file as the input.I am getting the following error message. Please help me with your suggestions on this. Thank you

Re: [gmx-users] protein membrane simulation

Hi all: Thanks a lot for replyng. You 're right, i include the popc.itp file in my .top and grompp runs well. I've changed to ffG43a2 force field, as David and Tsjerk said me, the ffG53a* isn't a good force field for lipids. The best of the gromos96 ff is ffG43a4 for membrane simulations, but

[gmx-users] hessian_matrix_from_ordered_trajectory

Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command trjorder to order the watermolecules in a way so that they are close to the center of mass of the

[gmx-users] modify C6 directly in FF using sigma and epsilon

Gromacs users, I'm using a force field (the port of AMBER to GROMACS) which uses combination rules (combination rule 2), etc. in terms of sigma and epsilon. However, I need to be able to modify C6 directly (in particular, I want to be able to set it to zero). Can anyone give me any pointers on a

Re: [gmx-users] protein membrane simulation

Hi Maite, You can use ffG45a3, which is an upgrade of ffG43a2; I've never heard of 43a4, but that's probably me. 45a3 and 43a2 are largely similar and AFAIK you don't need to renumber bonded interactions and such. Best, Tsjerk On 4/5/07, maite lopez [EMAIL PROTECTED] wrote: Hi all: Thanks a

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

David, How about adding [ nonbond_params ] in your ff???nb.itp file as shown in p.88 of the user's manual? I believe it will override the default vdw interaction for that particular atom-type pair. (Assuming you want to use combination rule #1 just for that atom-type pair) If I miss your point,

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

Ryogo Sugitani wrote: David, How about adding [ nonbond_params ] in your ff???nb.itp file as shown in p.88 of the user's manual? I believe it will override the default vdw interaction for that particular atom-type pair. (Assuming you want to use combination rule #1 just for that atom-type pair)

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

2007/4/5, David van der Spoel [EMAIL PROTECTED]: Ryogo Sugitani wrote: David, How about adding [ nonbond_params ] in your ff???nb.itp file as shown in p.88 of the user's manual? I believe it will override the default vdw interaction for that particular atom-type pair. (Assuming you want

Re: [gmx-users] hessian_matrix_from_ordered_trajectory

Hi Sang Min, The distance from the center of mass is not a proper identifier for these kinds of calculations. To do this properly, you have to map the water molecules to specific positions around your peptide, and base your identifiers on that. E.g. if you have: H2O-peptide--OH2 and

[gmx-users] Blue Gene compilation error cannot compute sizeof (int) 77

Howdy, I'm getting an error while running configure for Gromacs 3.3.1 on Blue Gene. checking size of int... configure: error: cannot compute sizeof (int), 77 I've searched the archives but haven't found anything that resolves the problem. I'm cross compiling this on the front end

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

Ryogo Sugitani wrote: 2007/4/5, David van der Spoel [EMAIL PROTECTED]: Ryogo Sugitani wrote: David, How about adding [ nonbond_params ] in your ff???nb.itp file as shown in p.88 of the user's manual? I believe it will override the default vdw interaction for that particular atom-type

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

David, I'm using 3.3/3.3.1. Is there an easy tweak to the source code that would allow something like this? i.e. could I somehow easily tweak the bit where it reads the nonbond_params section so I can use an alternate combination rule there by specifying, say, a different nonbonded parameter

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

David Mobley wrote: David, I'm using 3.3/3.3.1. Is there an easy tweak to the source code that would allow something like this? i.e. could I somehow easily tweak the bit where it reads the nonbond_params section so I can use an alternate combination rule there by specifying, say, a different

[gmx-users] DPPC bilayer simulation crash

I am trying to perform a simulation of 128 dppc in 3655 spc water. I obtained .pdb and .top files from the Biocomputing website at U.Calgary. I do nothing to alter the structure, which must be minimized as it comes from the end of a 1 ns simulation. Processing the input files works fine, but

Re: [gmx-users] hessian_matrix_from_ordered_trajectory

On Thu, 5 Apr 2007 18:53:58 +0200 Sang-Min Park [EMAIL PROTECTED] wrote: Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command trjorder to order the

Re: [gmx-users] protein membrane simulation

Hi Tsjerk: Of course, i was wrong, the force field i said is ffG45a4, not 43a4. In the article: A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6. (2004) Ostenbrink et al. refers that: The recent

RE: [gmx-users] modify C6 directly in FF using sigma and epsilon

Dear David, In fact I really did as you said. First prepare a top file which explicitly include all bonded and nonbonded terms according to combination rule. In this way that top file can be called stand-alone top file (all the necessary parameters all included). Then you can do what you want. In

RE: [gmx-users] modify C6 directly in FF using sigma and epsilon

Yes. I did this way. I wrote it in small awk script. If you like I can share with it. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856

RE: [gmx-users] Can you help me ?

It seems the ions type not set. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php

Re: [gmx-users] Can you help me ?

[EMAIL PROTECTED] wrote: when I use the following command ,there always a error message.Can you help me ? Thank you very much ! command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr error message: . . creating statusfile for 1 node... Back

Re: [gmx-users] DPPC bilayer simulation crash

Michael Skaug wrote: I am trying to perform a simulation of 128 dppc in 3655 spc water. I obtained .pdb and .top files from the Biocomputing website at U.Calgary. I do nothing to alter the structure, which must be minimized as it comes err, not minimized - sampled from the ensemble they were

[gmx-users] Re: please help me

[EMAIL PROTECTED] wrote: Dear Mark: thanks for your help. My topology file trp.top have included ions.itp and I think its contents match the topology file as far as atom and molecule names.what's It also needs to match the force field files you're using. more,trp.top and ions.itp