[gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs

Dear all. greetings. I need to know what force fields can I Choose to run: 1- ethanol vibrational mode. 2- B-DNA with 15 base pairs Thanks a lot for the response ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] rtp files

hi again please send me rtp file for phenylalanin- amide. thanks -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] rtp files

I beg your pardon. What do you think we are? The equivalent of a fast-food take-away? Or a service for doing your homework for you? Do take a good read of http://catb.org/~esr/faqs/smart-questions.html Tsjerk On Mon, Apr 21, 2008 at 1:28 PM, shahrbanoo karbalaee [EMAIL PROTECTED] wrote: hi

Re: [gmx-users] DCCM

Dear all, In some of the papers i read a cross-correlation analysis is meant to calculate the associated movements over the simulation for residues. A value of Cij is calculated which when +ve means that the given pair of atoms are moving together in the same direction and the same

RE: [gmx-users] DCCM

Hi, g_covar calculates the covariance matrix, which I guess is what you ask for. Berk. Date: Mon, 21 Apr 2008 18:05:41 +0530 Subject: Re: [gmx-users] DCCM From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Dear all, In some of the papers i read a cross-correlation analysis is

Re: [gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs

Collins Nganou wrote: Dear all. greetings. I need to know what force fields can I Choose to run: 1- ethanol vibrational mode. 2- B-DNA with 15 base pairs Start with a literature search. You'll need to do one later in order to defend your choice. Some person on a mailing list recommended it

[gmx-users] free energy calculation

Hi everyone, I want to calculate free energy between protein and ligand by g_lie command. So the average Coulomb interaction and average Lennard-Jones interaction of ligand-solvent are need. But I do not know if average Coulomb interaction is the result of Coul-SR plus Coul-14, which are

Re: [gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs

Mark Abraham wrote: Collins Nganou wrote: Dear all. greetings. I need to know what force fields can I Choose to run: 1- ethanol vibrational mode. 2- B-DNA with 15 base pairs Start with a literature search. You'll need to do one later in order to defend your choice. Some person on a mailing

[gmx-users] position restraints

Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: ...This usually means your system is exploding... Do you have any idea what may cause this

[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

Dear GROMACS users, particularly, those experienced with membrane simulations, I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain small solutes, much like what was done in A.K. Sum J.J. de Pablo, Biophys. J. 85, 3636 (2003) with DMSO. I'd like to use the TIP5P and OPLS

[gmx-users] 3.3.2 -b option not functioning as expected

Hello, I find that trjconv and g_order 3.3.2 don't properly find the frame to which I would like to seek via -b. I initially discovered this based on the output to the command line from g_order about which frame is being processed, and I have further confirmed that the incorrect frame is

Re: [gmx-users] 3.3.2 -b option not functioning as expected

Chris Neale wrote: Hello, I find that trjconv and g_order 3.3.2 don't properly find the frame to which I would like to seek via -b. I initially discovered this based on the output to the command line from g_order about which frame is being processed, and I have further confirmed that the

RE: [gmx-users] 3.3.2 -b option not functioning as expected

Hi, This is a known bug caused by autoconf, which has been worked around in 3.3.3. It turns out that a certain version of autoconf handles the definition of fseeko incorrectly, which causes Gromacs to use the wrong file offset. This only happens on certain system configurations. Unfortunately

[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

I use tip4p/opls/berger combination and it works well for me. I have never used tip5p. I suggest that you build your membrane and run one control simulation (sounds like you would lean toward using spc for this) and then one simulation with tip5p. Check order parameters and area per lipid while

[gmx-users] Re: the number of water molecules

How about using vmd selection within to do this Message: 3 Date: Sun, 20 Apr 2008 21:01:57 +0800 From: Dechang Li [EMAIL PROTECTED] Subject: [gmx-users] the number of water molecules To: gmx-users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;

[gmx-users] CNT

Hello, I plan to insert water molecules into a Single Wall NanoTube, I have generated the structure file of SWNT, but when I use: pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro to form the gro file, I got the following error: Fatal error: Residue 'UNK' not found in residue

RE: [gmx-users] CNT

You must define residue name UNK in your topology file. Hero [EMAIL PROTECTED] schrieb: Hello, I plan to insert water molecules into a Single Wall NanoTube, I have generated the structure file of SWNT, but when I use: pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro to form the gro

[gmx-users] 3.3.2 -b option not functioning as expected

Indeed, 3.3.3 works well. Thanks David and Berk. Chris. Chris Neale wrote: / Hello, // // I find that trjconv and g_order 3.3.2 don't properly find the frame to // which I would like to seek via -b. I initially discovered this based on // the output to the command line from g_order about

Re: [gmx-users] CNT

Quoting Hero [EMAIL PROTECTED]: Hello, I plan to insert water molecules into a Single Wall NanoTube, I have generated the structure file of SWNT, but when I use: pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro to form the gro file, I got the following error: Fatal error:

[gmx-users] request for default word-wrap on the mailing list

Is it possible for the moderators to change some setting that would automatically word-wrap all posts on the mailing list archive? Many of my posts end up spanning more than the horizontal space on one screen when viewed from the mailing list archive. I try to remember to add hard returns on

Re: [gmx-users] request for default word-wrap on the mailing list

[EMAIL PROTECTED] wrote: Is it possible for the moderators to change some setting that would automatically word-wrap all posts on the mailing list archive? This would be a good thing. It is also normally possible to set your own word wrap in an email client. Mark

RE: [gmx-users] water can't freeze

Dear Vasilii and other users, Thanks for you reply. I triedto do the simulation you said. But how to setup the initial configuration which is putting water contacting with ice, I knew in Gms tutor there is a example of mixed water and mathenol, it is a water box contacting

[gmx-users] Re: the number of water molecules (Jian Zou)

Message: 2 Date: Mon, 21 Apr 2008 10:43:27 -0400 From: Jian Zou [EMAIL PROTECTED] Subject: [gmx-users] Re: the number of water molecules To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 How about using vmd selection within to do this

[gmx-users] Re: CNT

Hello, when I follow http://cs86.com/CNSE/SWNT.htm and ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp I got the following message: Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds

[gmx-users] Range checking error

Dear gmx-users, I run MD for a protein molecule solvated with water molecules. Until now it works well, however strangely they started to crash, I don't know the reason. So, if anyone have similar problem please let me know the solution. It seems like that NPT system might cause some problems.

Re: [gmx-users] Range checking error

SeungPyo Hong wrote: Dear gmx-users, I run MD for a protein molecule solvated with water molecules. Until now it works well, however strangely they started to crash, I don't know the reason. So, if anyone have similar problem please let me know the solution. It seems like that NPT system

[gmx-users] Loop displacement calculation?

Dear gmx-users, (This is not related to my previous question about the failure of the simulation. Now I guess that there are some technical problems in our cluster system.) Hello gmx-users, I am not a quite new user, but still don't know many many thing. Planning an experiment I hope to listen

[gmx-users] free energy calculation

Hi everyone, I want to calculate free energy between protein and ligand by g_lie command. So the average Coulomb interaction and average Lennard-Jones interaction of ligand-solvent are need. But I do not know if average Coulomb interaction is the result of Coul-SR plus Coul-14, which are

[gmx-users] Fatal error: Could not write energies

HI gmx-users, Iam simulating POPC lipids in water,I have done minimisation,equilibration and production, Till 2ns ran fine but when iam trying to run 2.5 ns run mid of the simulation at 18650 step it crashed and showed error Pls suggest me my md.mdp file is title = popc_prod

Re: [gmx-users] Loop displacement calculation?

SeungPyo Hong wrote: Dear gmx-users, (This is not related to my previous question about the failure of the simulation. Now I guess that there are some technical problems in our cluster system.) Hello gmx-users, I am not a quite new user, but still don't know many many thing. Planning an

Re: [gmx-users] Fatal error: Could not write energies

sudheer babu wrote: HI gmx-users, Iam simulating POPC lipids in water,I have done minimisation,equilibration and production, Till 2ns ran fine but when iam trying to run 2.5 ns run mid of the simulation at 18650 step it crashed and showed error If the error is what's listed in your subject