[gmx-users] RMSIP (Root mean square inner products)?

Please tell me how gromacs calculates degree of overlap between conformational spaces of the two proteins is it from RMSIP (Root mean square inner products)? if yes then give me the reference in gromacs tutorial 4.0 -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] very low speed in simulation !( need for help)

Dear gmx-usres, In our university we have a cluster containing 20 nodes each with 4 processors, which I want to use that for the simulation project. As a test I submitted a run that I have tested it before in the Imperial College (London). Here the structure of the cluster is so that I should spe

[gmx-users] DSSP

Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local

Re: [gmx-users] very low speed in simulation !( need for help)

Hi, On May 18, 2010, at 9:35 AM, delara aghaie wrote: > Dear gmx-usres, > In our university we have a cluster containing 20 nodes each with 4 > processors, which I want to use that for the simulation project. > As a test I submitted a run that I have tested it before in the Imperial > College (

[gmx-users] Re: minimizing ligand only

Dear Justin, thank you for your answer. Actually I did the changes that you suggest, but the problem seems to be the fact that I called "lig" my molecule. In fact, the error message told that "The moleculetype lig is redefined". When I changed its name, it seemed to work. Is there some problem in G

[gmx-users] Re: OPLS-AA/L force field

Hi You Zou, Complementing Justin's message, I would invite you to take a look at acpype.googlecode.com. It's my attempt to address problems like yours. There's also links to some options besides ACPYPE. Bear in mind that you should know what you're doing. I would suggest you to read the Wiki's th

[gmx-users] Selecting groups for analysis in batch submission

Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give

[gmx-users] Re: minimizing ligand only

To the second question: PRODRG makes usually a very small box (sometimes smaller then the molecule, if i remember correctly), so if you want to use periodic boundary conditions you must make the box large enough, so that there are no problems with cut-offs. The easiest way to make the minimisat

[gmx-users] crystallographic water to tip4p model

Hi, I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set "-water tip4p" it protonates oxygens to spc water model instead. Is there any way to replace spc water molecules with tip4p water molecules in the same orientation? Btw what happen if I'l

[gmx-users] Selecting groups for analysis in batch submission

Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give

Re: [gmx-users] Selecting groups for analysis in batch submission

Anirban Ghosh wrote: Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from a

Re: [gmx-users] water medium

tahereh tekieh wrote: dear friends i want to simulate a water medium in which 5 types of different ions flow in it. how can i do that with gromacs? thanks Assuming they are monoatomic, you can use genion after you have added water. If they are polyatomic, use genbox -ci -nmol (before fil

Re: [gmx-users] Re: minimizing ligand only

Anna Marabotti wrote: Dear Justin, thank you for your answer. Actually I did the changes that you suggest, but the problem seems to be the fact that I called "lig" my molecule. In fact, the error message told that "The moleculetype lig is redefined". When I changed its name, it seemed to work.

Re: [gmx-users] DSSP

shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv

Re: [gmx-users] Selecting groups for analysis in batch submission

Thanks a lot Justin. On Tue, May 18, 2010 at 4:36 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> >> Hi ALL, >> >> I want to calculate the distance between a number of atom pairs using >> g_dist. For this I want to submit the job through a submission script so >> that g_dist calculat

[gmx-users] PLUMED release 1.2.0 available

The PLUMED Developers are proud to announce that the NEW version of PLUMED, version number 1.2.0, is available from http://merlino.mi.infn.it/plumed PLUMED is a plugin for free-energy calculations in molecular systems that can be interfaced with some of the most popular molecular dynamics codes

Re: [gmx-users] DSSP

Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fau

[gmx-users] Re: Need Help about GROMACS.

Thank you Dr. Justin for the reply. Here are the details of my simulation. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I am using 128 DPPC and 3655 water. The .pdb file is taken from Prof. Tieleman's p

Re: [gmx-users] DSSP

shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and giv

RE: [gmx-users] DSSP

Shahid, Before trying for "do_dssp" a gromacs utility calling dssp program , try first dssp program itself by passing simple input like pdb and I hope by that way you can resolve your problem B.Nataraj -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-

Re: [gmx-users] Re: Need Help about GROMACS.

Archana S Achalere wrote: Thank you Dr. Justin for the reply. Here are the details of my simulation. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I am using 128 DPPC and 3655 water. The .pdb file is

[gmx-users] simulated annealing (SA)

Hi gromacs users 1) after doing simulated annealing simulation, who can I understand that obtained structure is in global minimum and not in local minimum? 2) who can I understand that parameters used in mdp file (annealing_npoints, annealing_time, annealing_temp) are true? Any help will highly

Re: [gmx-users] DSSP

Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time

Re: [gmx-users] DSSP

shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.ma

[gmx-users] PCA

I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows: 1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix? 2

[gmx-users] Re: Need Help about GROMACS.

I think the force I have applied on the two systems balance each other. If I calculate total force on each group: DPPC = 734 amu, water = 18 amu 734*128 = 93952 (This thing you calculated as 90282) 18*3655 = 65790 93952*0.07 = 6576.64 65790*0.1 = 6579 If I reduce values of acceleration

Re: [gmx-users] Re: Need Help about GROMACS.

Archana S Achalere wrote: I think the force I have applied on the two systems balance each other. If I calculate total force on each group: DPPC = 734 amu, water = 18 amu 734*128 = 93952 (This thing you calculated as 90282) Ah yes, typo. Sorry :) 18*3655 = 65790 93952*0.07 = 6576.64

[gmx-users] making index file

Hi, could you guide me how one can create .ndx file format. I thought it would be accessible in library directory like rtp ..files. Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

Re: [gmx-users] making index file

Moeed skrev: Hi, could you guide me how one can create .ndx file format. I thought it would be accessible in library directory like rtp ..files. Thanks, Use make_ndx to create a ndx file. The format is pretty straightforward and the files themselves quite readable. Not enoyable, mind you, bu

Re: [gmx-users] Computational Alanine Scanning

When you re-generate hydrogens, you are introducing some extra disorder to the system. What I did is to write a script to rename the hydrogens. For example, there are residues that have the hydrogen numbering starting from 2 (eg. hydrogens on CB of lysine had hydrogens starting from HB2). In the sc

Re: [gmx-users] RMSIP (Root mean square inner products)?

- Original Message - From: pawan raghav Date: Tuesday, May 18, 2010 17:34 Subject: [gmx-users] RMSIP (Root mean square inner products)? To: gmx-users@gromacs.org > Please tell me how gromacs calculates degree of overlap between > conformational spaces of the two proteins is it from RMS

Re: [gmx-users] crystallographic water to tip4p model

- Original Message - From: Павел Кудрявцев Date: Tuesday, May 18, 2010 20:55 Subject: [gmx-users] crystallographic water to tip4p model To: gmx-users@gromacs.org > Hi, > I wanna keep crystallographic water with tip4p model for md simulation but > when I use pdb2gmx even if I set "-wate

Re: [gmx-users] simulated annealing (SA)

- Original Message - From: shahab shariati Date: Tuesday, May 18, 2010 23:36 Subject: [gmx-users] simulated annealing (SA) To: gmx-users@gromacs.org > Hi gromacs users >   > 1) after doing simulated annealing simulation, who can I understand that > obtained structure is in global minim

[gmx-users] RE: gmx-users Digest, Vol 73, Issue 109

Dear Friends I tried to obtain the XY density maps of the heme using g_densmap tool. The molecule was centered in the box The system was rotated to maintain the XY plane on the molecular plane. In the reference gro file, the molecule was also centered and the plane XY was on the molecula

[gmx-users] how to define an index file

Hello, I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system. To do this how should I define my index groups. Should I include all 125 molecuels in index file? now I have only the first 20 atoms (first mo

Re: [gmx-users] how to define an index file

- Original Message - From: Moeed Date: Wednesday, May 19, 2010 4:41 Subject: [gmx-users] how to define an index file To: gmx-users@gromacs.org > Hello, > > I am trying to create an index file to get interaction energies between > hexane (C6H14, 20atoms) molecules. I have 125 hexane mo

Re: [gmx-users] Using g_densmap

Please use a descriptive subject line to help everybody. I suspect your use editconf is your problem. -princ may not preserve your box the way you've assumed. Try -princ -c, or editconf -princ then editconf -c. It's also pointless and error-prone to compile MPI versions of the GROMACS tools. On

[gmx-users] energygrp_excl and grompp warning

Hi all, I try to use the energy exclusion keyword in the MDP file: energygrp_excl = CNT CNT and got the warning - WARNING 2 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups What can be the source of this issue? BTW, there are only LJ i

Re: [gmx-users] energygrp_excl and grompp warning

Vitaly Chaban wrote: Hi all, I try to use the energy exclusion keyword in the MDP file: energygrp_excl = CNT CNT and got the warning - WARNING 2 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups What can be the source of this issue?

[gmx-users] Re: how to define an index file

> > I am trying to create an index file to get interaction energies between > hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my > system. > To do this how should I define my index groups. Should I include all 125 > molecuels in index file? now I have only the first 20 atoms (firs

Re: [gmx-users] Re: how to define an index file

Vitaly Chaban wrote: I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system. To do this how should I define my index groups. Should I include all 125 molecuels in index file? now I h

[gmx-users] reading velocity in the g_msd routine

Hello gmx-users users :) I am modifying the 'g_msd' utility to be able to calculate viscosities using the corresponding Einstein relationship according to equation 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is similar to the mean-square displacement equation for self-diffusion

Re: [gmx-users] reading velocity in the g_msd routine

On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel wrote: > Hello gmx-users users :) > > I am modifying the 'g_msd' utility to be able to calculate viscosities > using the corresponding Einstein relationship according to equation > 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is > sim

[gmx-users] problem with index file

Hello, I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules (interaction energy between two hexane molecules) I have 125 hexane molecules in my system. Please help me figure out what the problem is. make_ndx -f Hexane-Stack125.gro -o index.ndx

Re: [gmx-users] problem with index file

Moeed wrote: Hello, I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules (interaction energy between two hexane molecules) I have 125 hexane molecules in my system. Please help me figure out what the problem is. make_ndx -f Hexane-Stack

[gmx-users] 转发: [gmx-user]Error by pdb 2gmx

Dear Yanmei Song： I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When I run pdb2gmx using my molecules with the command:   "pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3"    I got the error message: "  Opening library file ffG45a3.rtp   Opening li

[gmx-users] [gmx-user]Error by pdb2gmx

Dear Yanmei Song： I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When I run pdb2gmx using my molecules with the command:   "pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3"    I got the error message: "  Opening library file ffG45a3.rtp   Opening library file 

Re: [gmx-users] [gmx-user]Error by pdb2gmx

- Original Message - From: 佘安奇   Date: Wednesday, May 19, 2010 16:17 Subject: [gmx-users] [gmx-user]Error by pdb2gmx To: gmx-users@gromacs.org --- | > Dear Yanmei Song： > I used gromacs version 3.3.1. I update ffG45a3.rtp to includ

[gmx-users] RMSIP

Thanks mark, but I think that g_anaeig calculates the degree of overlap then what method would you use to calculate this? -- Pawan -- 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 bef