Re: [gmx-users] Pull to separate dimer

Ragnarok sdf wrote: I am trying to learn how to use the pull code to separate a dimer. I have read gromacs 4 manual and a tutorial I found on CSC, but it seems I still haven´t got the knack. My system is consisted of a dimer inserted into a membrane lipid bilayer. I have included the followin

Re: [gmx-users] Graphene Sheet Rolling up into CNT

Justin A. Lemkul wrote: Darrell Koskinen wrote: Hey GROMACS Gurus, I was wondering if you could enlighten me. I performed a simulation of a graphene sheet in an ammonia gas at 240K using ffoplsaa parameters and see that the graphene sheet begins to curl up into what appears to be a nanotube

[gmx-users] Pull to separate dimer

I am trying to learn how to use the pull code to separate a dimer. I have read gromacs 4 manual and a tutorial I found on CSC, but it seems I still haven´t got the knack. My system is consisted of a dimer inserted into a membrane lipid bilayer. I have included the following lines into my mdp parame

Re: [gmx-users] Graphene Sheet Rolling up into CNT

Darrell Koskinen wrote: Hey GROMACS Gurus, I was wondering if you could enlighten me. I performed a simulation of a graphene sheet in an ammonia gas at 240K using ffoplsaa parameters and see that the graphene sheet begins to curl up into what appears to be a nanotube. I did not run the simul

[gmx-users] Graphene Sheet Rolling up into CNT

Hey GROMACS Gurus, I was wondering if you could enlighten me. I performed a simulation of a graphene sheet in an ammonia gas at 240K using ffoplsaa parameters and see that the graphene sheet begins to curl up into what appears to be a nanotube. I did not run the simulation long enough to actual

Re: [gmx-users] Gaussian network model (GNM) ?

Chih-Ying Lin wrote: Hi Is Normal mode analysis from Gaussian network model (GNM) ? Did you look in the manual first? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

YH wrote: > Dear Dr. Saavedra, > > I would like to ask your help for my use of Gromacs. > Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems > like the following. > Would you please tell me how to sovle it. > > Thank you very much in advanc, > > James, Wang(Dr.) > Da

[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

Dear Dr. Saavedra, I would like to ask your help for my use of Gromacs. Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems like the following. Would you please tell me how to sovle it. Thank you very much in advanc, James, Wang(Dr.) Dalian university of Technology,

[gmx-users] Gaussian network model (GNM) ?

Hi Is Normal mode analysis from Gaussian network model (GNM) ? Thank you Lin ___ 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 postin

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Mark, Thanks for the information. Actually in 7.4 I found only g_rotacf and g_angle also g_sgangle that calculate rotation and angle correlation function and in appendix D I could not find related topic... I appreciate if someone gives me more detail to do the job. I want to

Re: [gmx-users] A charge group moved too far between two domain decompostion steps

Chih-Ying Lin wrote: Hi A charge group moved too far between two domain decompostion steps What does this sentence mean? What is the domain decompostion step? How to make change about the domain decompostion steps? Start with reading 3.17 of the manual. Mark

Re: [gmx-users] correlation function

Hi Mark, Thanks for the information. Actually in 7.4 I found only g_rotacf and g_angle also g_sgangle that calculate rotation and angle correlation function and in appendix D I could not find related topic... I appreciate if someone gives me more detail to do the job. I want to calculate that R is

[gmx-users] Re: Infiniband Setup Benchmark Results

I just setup an infiniband networking system on my Dell dual quad core cluster and wanted to share the benchmark results. I am using a Cisco SFS 7000P switch and Mellanox MHEA28-XTC HCA infiniband cards. Setup was trivial thanks to a very competent sys admin Used open the openMPI that came with

Re: [gmx-users] A charge group moved too far between two domain decompostion steps

Chih-Ying Lin wrote: Hi A charge group moved too far between two domain decompostion steps What does this sentence mean? It means that something is careening across your system, probably moving across a domain too fast. What is the domain decompostion step? Probably the frequency

[gmx-users] A charge group moved too far between two domain decompostion steps

Hi A charge group moved too far between two domain decompostion steps What does this sentence mean? What is the domain decompostion step? How to make change about the domain decompostion steps? Thank you Lin ___ gmx-users mailing listgmx-users

Re: [gmx-users] A charge group moved too far between two

Chih-Ying Lin wrote: Hi I was currently updatiing the 3.3.3 version to 4.0.5 version. My system is "one protein + TIP3P water". The protein structure is from 6LYZ.pdb The ,gro file and .top file are created from pdb2gmx. Then, I do the following steps, Energy minimization of the structure (v

[gmx-users] A charge group moved too far between two

Hi I was currently updatiing the 3.3.3 version to 4.0.5 version. My system is "one protein + TIP3P water". The protein structure is from 6LYZ.pdb The ,gro file and .top file are created from pdb2gmx. Then, I do the following steps, Energy minimization of the structure (vacuum) Periodic boundary

[gmx-users] Re: please help me on last query

abhijit kayal wrote: Hi As you said I generated a pdb file of n-butane in PRODRG . I am executing following command. pdb2gmx -f ALA.pdb -p ALA.top -o ALA.gro It is successfully working on amino acid residue. But when i am executing for butane. pdb2gmx -f BUTANE.pdb -p BUTANE.t

Re: [gmx-users] how to create topology file for butane

simon sangma wrote: Respected sir, I am working on GROMACS. I need your help.I am trying to generate topology file for non-standard molecules like butane, water. I am executing following command. *pdb2gmx -f ALA.pdb -p ALA.top -o ALA.gro* ** It is successfully working on

[gmx-users] how to create topology file for butane

Respected sir, I am working on GROMACS. I need your help.I am trying to generate topology file for non-standard molecules like butane, water. I am executing following command. *pdb2gmx -f ALA.pdb -p ALA.top -o ALA.gro* ** It is successfully working on amino acid residue.

Re: [gmx-users] Normal mode analysis

simon sangma wrote: Hi! I am a user of gromacs. Could someone provide me with a method (or set of commands) for normal mode analysis of small molecules (water, n-butane, etc). Also could you please provide a command for generating Hessian Matrix after the energy minimization. You should st

[gmx-users] Re: Help me about GROMACS

Hi, With regards to the question about my tutorial, you have not taken care to update your topology through the steps of preparing the system. Using the -p flag with genbox and genion will make these changes for you, as is instructed in the tutorial. With regards to your other question, pl

[gmx-users] Normal mode analysis

Hi! I am a user of gromacs. Could someone provide me with a method (or set of commands) for normal mode analysis of small molecules (water, n-butane, etc). Also could you please provide a command for generating Hessian Matrix after the energy minimization. _

Re: [gmx-users] tables

zhangjianguo2002 wrote: Thanks,Mark I have read section 6.7 of the version 4.0 ,I find that somethings different from the manual of version 3.3, in version 4.0, the f' replaces f'',that means that column is the first derivative of the potential,that is force,am I right? Yes, they are differ

[gmx-users] table problems

Hi evergy one, I am trying to study a single type particle system using tabulated function, so I set its type as 'C', but when mdrun step, it stoped, the feedback messages as follows: *** Reading file phenyl_em.tpr, VERSION 4.0.4 (single precision) Loaded with Money MPI process rank 0 (

[gmx-users] Re: gmx-users Digest, Vol 64, Issue 138

Jamie, How do you like g_vellacc or g_dipoles? :) Best, Vitaly > > Dear all, > Is there any tool in gromacs that can calculate time correlation > function ??? R(x,y,z). Many Thanks in Advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re:gmx-users Digest, Vol 64, Issue 126

Thanks,Mark I have read section 6.7 of the version 4.0 ,I find that somethings different from the manual of version 3.3, in version 4.0, the f' replaces f'',that means that column is the first derivative of the potential,that is force,am I right? >zhangjianguo2002?wrote: >>?Dear, >>?? >>???