[gmx-users] No convergence in Diffusion Coefficient

On 2010-06-29 05.50, Igor Leontyev wrote: See the table bellow, there is no convergence of the Self-Diffusion Coefficient (Dself) over the trajectory length. Dself is obtained for NPT box of 1024 SPC/E water molecules by the Einstein's relation (via RMSD). In Gromacs Manual or AlienTildesley's

Re: [gmx-users] B-factor

- Original Message - From: shahab shariati shahab.shari...@gmail.com Date: Tuesday, June 29, 2010 15:51 Subject: [gmx-users] B-factor To: gmx-users@gromacs.org Dear Erik Marklund thanks for your attention I saw www.pdb.org. there is b-factor in pdb files being in this website

[gmx-users] Simulatimg two proteins in water system

H Everybody ther, I am simulating two already docked proteins which are in a single .pdb file to study the aggregation behavior. Doing for the first time, I have tried with and without TER option too. There are 28 residues and 240 atoms in first chain A and same number of atoms in chain B.

Re: [gmx-users] Simulatimg two proteins in water system

- Original Message - From: radhika jaswal jaswalradh...@yahoo.co.in Date: Tuesday, June 29, 2010 16:30 Subject: [gmx-users] Simulatimg two proteins in water system To: gmx-users@gromacs.org --- | H Everybody ther, I am

[gmx-users] g_msd and diffusion coefficent

Hi gromacs users in my system, there are pr, dna, water and Na and I want to obtain diffusion of pr in dna but when I use g_msd command, gromacs says select only 1 group. should be this group pr or dna? Thanks a lot in advance. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] g_msd and diffusion coefficent

- Original Message - From: leila karami karami.lei...@gmail.com Date: Tuesday, June 29, 2010 16:41 Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org Hi gromacs users in my system, there are pr, dna, water and Na and I want to obtain diffusion of pr in

[gmx-users] g_msd and diffusion coefficent

Dear Mark Abraham yes. pr means protein. I want to obtain diffusion of protein within dna. I want to know how/how much pr diffuse to dna. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] g_msd and diffusion coefficent

- Original Message - From: leila karami karami.lei...@gmail.com Date: Tuesday, June 29, 2010 17:32 Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org Dear Mark Abraham yes. pr means protein. I want to obtain diffusion of protein within dna. I want to

[gmx-users] g_msd and diffusion coefficent

Dear Mark Abraham No, I want to measure something about the diffusion of my protein to DNA (especially to major groove of DNA) in the presence of water (as solvent). -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] Technical

Dear Justin, Thanks for the wonderful suggestions which is very clear and informative but I am confused about some points below 1. Actually my protein is human mitochondrial protein so I have used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the condition applied, so I don't

[gmx-users] Re: g_msd and diffusion coefficent

Use NDX file. Dr. Vitaly V. Chaban in my system, there are pr, dna, water and Na and I want to obtain diffusion of  pr in dna but when I use g_msd command, gromacs says select only 1 group. should be this group pr or dna? -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] liquid-vapor

Hi, Is there a standard trick in gromacs to get the atom numbers which are located in the liquid-vapor interface? Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

[gmx-users] g_msd and diffusion coefficent

Dear Vitaly Chaban I know using index file but gromacs say : select only 1 group. what is this group ? protein? or DNA? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] g_msd and diffusion coefficent

- Original Message - From: leila karami karami.lei...@gmail.com Date: Tuesday, June 29, 2010 18:08 Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org Dear Mark Abraham No, I want to measure something about the diffusion of my protein to DNA (especially to

Re: [gmx-users] error while loading shared libraries: libOpenMM.so:

Hi, You also need the OpenMM libraries and plugins. For more detail see: http://www.gromacs.org/gpu#Installing_and_running_Gromacs-GPU -- Szilárd On Sat, Jun 26, 2010 at 6:18 PM, Tarsis tarsis.b...@epm.br wrote: I'm trying to install cuda but when I export

[gmx-users] Re:g_msd and diffusion coefficent

Message: 5 Date: Tue, 29 Jun 2010 11:54:12 +0330 From: leila karami karami.lei...@gmail.com Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org Message-ID:        aanlktinlxdcdfo3ytlz_zcy-ppgr8b6jnwhc3fc7t...@mail.gmail.com Content-Type: text/plain;

[gmx-users] Re: gromacs with CMAP

HI, David, thanks for your advise. I remove the bond angle force and get same result. It is really strange. If I set +5 on all the 24*24 grid, I just get a inverted distribution and if I set 0 on all grid, I will get a uniformed distribution. It is like that 27 regions are force to have zero cmap

Re: [gmx-users] Re: gromacs with CMAP

Hi, I do not fully understand what you are trying to do, but currently CMAP is only available for the standard amino acid residues present in the rtp-file for the Charmm-forcefield, and the values for the grid are specified in the cmap.itp-file. Do you use something else? /Per 29 jun 2010

Re: [gmx-users] Re: gromacs with CMAP

It is because I want to apply cmap to my own stuff. I can define my own 2D grid potential and apply to two sequential dihedral angles by add one line in the topol file. However, the testing result is really unexpected. dawei On Tue, Jun 29, 2010 at 8:53 AM, Per Larsson per.lars...@sbc.su.se

[gmx-users] multiple time step

Dear All, Is it possible to carry out  multiple time step  molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing list

[gmx-users] different ref_t

I try to simulate a small peptide in CHCl3 there the peptide is couplet to a heat bath at a different temperature: tcoupl = nose-hoover tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.01 0.01 ref_t = 220 300 If I do so the temperature of the

Re: [gmx-users] Technical

pawan raghav wrote: Dear Justin, Thanks for the wonderful suggestions which is very clear and informative but I am confused about some points below 1. Actually my protein is human mitochondrial protein so I have used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the

[gmx-users] g_rdf has a huge memory leak.

Hi everyone: I am using g_rdf to calculate radial distribution function. However when I check the memory usage using top, it seems to me that the code has a huge memory leak. My system has 4GB memory but it usually has 40MB free memory left after the program finishes. Does anyone have the same

Re: [gmx-users] g_rdf has a huge memory leak.

Hi Kun, Can you tell more about what you are doing? What are you analyzing? How large is the system? Which groups do you use for analysis. Etc., etc. Now, you might be right, but you might as well be jumping to conclusions. Cheers, Tsjerk On Tue, Jun 29, 2010 at 4:12 PM, Kun Huang

[gmx-users] multiple time step

multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for

[gmx-users] different ref_t

Can you please supply gen_temp and also your pressure coupling values? Also, please supply the g_energy values that show the temperatures changing as you suggest (with accompanying timestep info). I'm fairly sure that what is happening is that you are simply seeing the nose-hoover

Antw: [gmx-users] multiple time step

Hallo, I would try to use the program protomol. There are many possibilities for performing multiple timestepping. Emanuel oguz gurbulak 29.06.10 15.41 Uhr Dear All, Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you

[gmx-users] Re: multiple time step

Chris, An interesting question... BTW, is there any philosophy of gromacs developers to avoid this algorithm in the MD engine? Vitaly multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out  multiple time step  

Re: [gmx-users] Re: multiple time step

Hi, The core developers have the answer for this one, but I can make an educated guess: Implementing it would mean a LOT of work and the rewards are small. The latter because most particles will have rougly the same oscillation period if one uses all-atom forcefields and turn on virtual

[gmx-users] ED sampling

Hi I need some information about how ED sampling works when a subset of the atoms are used for covariance analysis. Basically I would like to move the system along the first eigenvector obtained from covariance analysis of the C-alpha atoms only. From the paper Toward an Exhaustive Sampling

[gmx-users] Mixed Solvents Preparation?

Dear Gromas users, I want to run another set of MD simulation of my polymer in a mixed solvent. step 1 24 polymer molecules in a 10 * 10 * 10 nm of box. step 2 I want to add 50% (v/v) of two solvents to this box. I have already done an MD simulation with their individual solvents, now I

[gmx-users] Re: Mixed Solvents Preparation?

tekle...@ualberta.ca wrote: Dear Gromas users, I want to run another set of MD simulation of my polymer in a mixed solvent. step 1 24 polymer molecules in a 10 * 10 * 10 nm of box. step 2 I want to add 50% (v/v) of two solvents to this box. I have already done an MD simulation with

[gmx-users] REMD

Dear Justin, No dear I have not modelled the membrane, my protein is a simple protein which contained a loop about 59 amino acids. So I am intrested to model this loop through MD simulation. In this concerned I did 15 ns simulations, but right now don't know how to perform sampling for my protein

[gmx-users] Replicating monomer units

Hello Justin, I spent a full day to find a proper value for -d but it seems there is no way of getting correct bond lenght and angle at the same time. With the following commands I am getting correct bond length for the atoms connecting two monomer units but the angle is 140. I get 110 angle

Re: [gmx-users] Replicating monomer units

Moeed wrote: Hello Justin, I spent a full day to find a proper value for -d but it seems there is no way of getting correct bond lenght and angle at the same time. With the following commands I am getting correct bond length for the atoms connecting two monomer units but the angle is 140.

[gmx-users] Script for detecting interfaces

A couple of months ago someone mentioned a recent publication that went through a procedure for the detection of an interface / surface between phases for data from MD. Remember reading the publication and thinking was pretty neat and need to come back and try it. Well, for the life of me can't

[gmx-users] automating analysis using shell scripting

Dear Gromacs users, This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those distances. The problem I

Re: [gmx-users] automating analysis using shell scripting

Hassan Shallal wrote: Dear Gromacs users, This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those

RE: [gmx-users] automating analysis using shell scripting

Thanks Justin, this is just working amazingly From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Tue 6/29/2010 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] automating analysis using shell scripting Hassan

Re: [gmx-users] mdrun_mpi issue.

- Original Message - From: quantrum75 quantru...@yahoo.com Date: Wednesday, June 30, 2010 7:12 Subject: [gmx-users] mdrun_mpi issue. To: gmx-users@gromacs.org --- | Hi Folks, I am trying to run a simulation under GMX 4.0.5. When

[gmx-users] REMD

Dear Justin, I have read manual there was an equation where T1 and T2 are the two temperatrure will be assign but in my case I don't have different temperature. I have to simulate at same temperature. Is there any other alternative to perform sampling rather than REMD. I am working on one

Re: [gmx-users] REMD

- Original Message - From: pawan raghav pwnr...@gmail.com Date: Wednesday, June 30, 2010 14:56 Subject: [gmx-users] REMD To: gmx-users@gromacs.org Dear Justin, I have read manual there was an equation where T1 and T2 are the two temperatrure will be assign but in my case I don't

[gmx-users] multiple time step

I recall seeing something online about how gromacs developers have decided to focus on increasing the overall speed and allowing generally large timesteps (via e.g. angle constraints) vs. implementing multiple timestepping (no mailing list ref. sorry). I agree that this is not a logically