[gmx-users] announcement: Advanced Gromacs workshop in Goettingen September 24-26

Hi, As promised, there will be a second gromacs workshop this year. The workshop will be held at the Max Planck Institute for biophysical chemistry in Goettingen, Germany from 24 to 26 september. As in the previous workshop in Stanford, the idea is to bring together people experienced with

Re: [gmx-users] Force field parameters in water or in vacuum?

[EMAIL PROTECTED] wrote: Please don't post to the users list and the developers list simultaneously with the same question. I think this is more appropriately a users list question. I guess if you also get a reply on the developers list then it pays to post to both, but the idea is to put it o

[gmx-users] Force field parameters in water or in vacuum?

Please don't post to the users list and the developers list simultaneously with the same question. I think this is more appropriately a users list question. I guess if you also get a reply on the developers list then it pays to post to both, but the idea is to put it only in one space. H

Re: [gmx-users] Re: Force field parameters in water or in vacuum?

Chih-Ying Lin wrote: Hi for 45a3 force field, is it created in vacuum / in water or solution ? Justin said the most of the force field is defined as condensed phase ??? Do you mean the liquid phase / or in water phase ? Check the GROMACS manual for literature references for this and other for

[gmx-users] Re: Force field parameters in water or in vacuum?

Hi for 45a3 force field, is it created in vacuum / in water or solution ? Justin said the most of the force field is defined as condensed phase ??? Do you mean the liquid phase / or in water phase ? Thanks Lin Message: 7 Date: Thu, 22 May 2008 13:13:37 -0400 From: "Justin A. Lemkul" <[EMAIL

Re: [gmx-users] Simulate the organic molecule => input / output error

Chih-Ying Lin wrote: Hi Does the Gromacs only recognize the residues in the pdb file? No... but pdb2gmx will only build a topology in an automated fashion if the residues are present in its databases. If they are not the standard amino acids in the library, Gromacs can't read, right??? A

[gmx-users] Simulate the organic molecule => input / output error

Hi Does the Gromacs only recognize the residues in the pdb file? If they are not the standard amino acids in the library, Gromacs can't read, right??? Or, how does the Gromacs simulate the organic molecule? The command pdb2gmx could not produce the top and the gro file. Instead, it shows that "

RE: [gmx-users] how to edit pdb file

Hi Justin, This command is just what I wanted. Thanks a lot. Hi Yang,Andrea and Alan, Thanks for your help. The link for PDB format is very useful.And I think Xemacs will be helpful for future use. Best regards, xiupeng From: [EMAIL PR

Re: [gmx-users] Unable to minimize energy

Paul Whitford wrote: This is likely an embarrassingly trivial problem, but let's see. I am following the energy minimization scheme presented in the groningen tutorial http://md.chem.rug.nl/education/mdcourse/MDpract.html I believe I follow the directions exactly, yet I can not minimize belo

Re: [gmx-users] Error while running starting grompp and mdrun

Ragothaman Yennamalli wrote: Dear Mark, Thanks for the mail. Since there's three different usages of -np you'd need to be more precise to make a good description of your problem. I was changing the -np option in mdrun and grompp. The symptoms you observe make sense if $NSLOTS==1. Since

Re: [gmx-users] Force field parameters in water or in vacuum?

Chih-Ying Lin wrote: Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, wil

[gmx-users] Unable to minimize energy

This is likely an embarrassingly trivial problem, but let's see. I am following the energy minimization scheme presented in the groningen tutorial http://md.chem.rug.nl/education/mdcourse/MDpract.html I believe I follow the directions exactly, yet I can not minimize below Fmax~500 I download 1A

Re: [gmx-users] Force field parameters in water or in vacuum?

Quoting Chih-Ying Lin <[EMAIL PROTECTED]>: > Hi > For one molecule, will Gromacs give the same set of force field > parameters to this molecule no matter this molecule is put in water or > in vacuum? Depending on what's defined within the specific force field, yes. For example, ffG43b1 is a "vac

[gmx-users] Force field parameters in water or in vacuum?

Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, will the force field param

Re: [gmx-users] Implicit Solvent Simulations

Hello Una (and everyone else) I'm happy to announce that, while not yet available in cvs, it will very soon be possible to do implicit solvation with Gromacs. I'm have a working implementation almost finished, and are currently running some tests to assure that the code is stable. With any

[gmx-users] Implicit Solvent Simulations

To the Gromacs user community, As of April 2007 it was not possible to do implicit solvent MDs with Gromacs (http://www.gromacs.org/pipermail/gmx-users/2007-April/026849.html). Has this changed since then? Kind regards, Una -- Una Bjarnadottir School of Biomolecular and Biomedical Sc

Re: [gmx-users] Error while running starting grompp and mdrun

Dear Mark, Thanks for the mail. > > Since there's three different usages of -np you'd > need to be more > precise to make a good description of your problem. > I was changing the -np option in mdrun and grompp. > The symptoms you observe make sense if $NSLOTS==1. Since > all three -np > fla

Re: [gmx-users] Error while running starting grompp and mdrun

Ragothaman Yennamalli wrote: Dear all, I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 processors. I am submitting the job via a SGE script. After, I submit the job by "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell

Re: [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)

Nadir Kaplan wrote: What is going on here? How can I get velocity info? Any help will be greatly appreciated. Note that, there is an external acceleration on the water molecules, where is the position of CNT is fixed. So obviously water molecules should have finite velocities. Turn off the weir

[gmx-users] Error while running starting grompp and mdrun

Dear all, I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 processors. I am submitting the job via a SGE script. After, I submit the job by "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell me how to troubleshoot this p

Re: [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)

Dear Mark, I am doing a simulation of a carbon nanotube (CNT) inside water. First I am going to describe my problem and then give info about my simulation setup (initial conditions, parameters, etc.). My problem is as follows: (1) I am doing a *.gro file of a *.pdb of a (16,16) CNT, without

Re: [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)

Dear Justin, The reply is below: I am doing a simulation of a carbon nanotube (CNT) inside water. First I am going to describe my problem and then give info about my simulation setup (initial conditions, parameters, etc.). My problem is as follows: (1) I am doing a *.gro file of a *.pdb of a

Re: [gmx-users] generation of amorphous surface

h a wrote: Dear users, I'm using Gromacs to generate polymer surface. Is it possible using genbox command ? As I see genbox is used to create a box filled with Correct. editconf can do basic replication of a periodic image, however. Mark ___ gmx-

[gmx-users] generation of amorphous surface

Dear users, I'm using Gromacs to generate polymer surface. Is it possible using genbox command ? As I see genbox is used to create a box filled with solvent. thank you, Sincerely Harshith ___ gmx-users mailing listgmx-users@gromacs.org http://www.

Re: [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field

wang kelvin wrote: Hi, everyone. I am simulating DMSO. At fisrst ,bond parameters contain two c-c bonds,and c-o bond ,which actually not in existence. But gmx 's force field ffg53a6 documents in top directory defines these bonds. When running mdrun , system reminds "segmentation default". the

Re: 回复： Re: [gmx-users] how to remd an alysi?

xi zhao wrote: > I performed remd using GROMACS 3.3.1 at four different temperatures: > 270k, 400k, 540k, 660k, and produced four trajectories. I want to know > whether my simulation is ok, but I do not know how to analysis my > trajectories. Probably these temperatures are spaced far too wide