Re: [gmx-users] Using many index file in one command line

Use make_ndx to put all your groups in one .ndx file. It's totally unnecessary to use multiple .ndx file in one command. Terry On Tue, May 28, 2013 at 10:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear users, Is there command for using many different index.ndx files in one command

Re: [gmx-users] aligning problem

Check this: http://manual.gromacs.org/online/editconf.html editconf -align On Fri, Jan 25, 2013 at 1:12 PM, 申昊 shen...@mail.bnu.edu.cn wrote: Dear GMX users, I have a question about aligning my molecules along specific coordinate axis ,such as Z-axis. Does anyone know the codes?

Re: [gmx-users] the CPU of REMD

The TOTAL number of cores is specified by -np option. So it's 8 in all. By the way, you can submit the job to see how. It'd be faster than waiting on the list. Terry On Thu, Oct 18, 2012 at 3:20 PM, Albert mailmd2...@gmail.com wrote: hello: I've got a qeustion the CPU for replica exchange

Re: [gmx-users] how to compile double precision of 4.6?

http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#double_precision_build Terry On Thu, Oct 18, 2012 at 3:07 PM, Albert mailmd2...@gmail.com wrote: hello: I found with the default parameters of cmake, we can only get the single precision gromacs 4.6. I am wondering how

Re: [gmx-users] Missing charges in a .gro file

/gro.html http://manual.gromacs.org/online/top.html There are no charges in .gro files. The charges are probably discarded in your way. Terry gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] solvent group size (12548) is not a multiple of 3

On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap sang...@imtech.res.inwrote: Hello all I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC) I am geeting error during addiotion of ions Fatal error: Your solvent group size (12548) is not a multiple of 3 For more information and

Re: [gmx-users] problem

You should paste your topology for you metal halides so that others can help. On Fri, May 11, 2012 at 9:48 PM, Anik Sen anik...@csmcri.org wrote: Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. I was trying to run the dynamics for some inorganic metal halides

Re: [gmx-users] nodes error

Hi, You should start from here: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Terry On Fri, Jan 6, 2012 at 12:49 PM, Albert mailmd2...@gmail.com wrote: Hello: I found

Re: [gmx-users] Re: nodes error

on the information you provided, the only thing I can say is, MAYBE your system is too small to run with 256 processors. Cheers Terry On Fri, Jan 6, 2012 at 3:45 PM, Albert mailmd2...@gmail.com wrote: thank you very much for kind reply. I change my command as following: mpirun -exe /opt

Re: [gmx-users] how to select option for genion command automatically?

This is what you are looking for: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting Terry On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang liu4...@gmail.com wrote: I am wondering if there is a flag to make the command select SOL automatically instead

Re: [gmx-users] non-interactive script help

You should issue a q command to save and quit. So choice.txt should look like: ri 1-20 ... ... ri 101-120 q Cheers. Terry On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury iitd...@gmail.comwrote: Hi gmx-users, I was trying to feed make_ndx with the non-interactive script, below is my

Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

Hi Chuan, Leap is a part of Ambertools which is free. See http://ambermd.org/#AmberTools Good luck. Terry 2011/4/20 Liao Chuan liaoch...@tju.edu.cn HI, Itamer and Mark, thanks for your prompt replies. Pymol, Amber and Sybyl are commercial software. Any free software/scripts? - Chuan

[gmx-users] Strange behavior from g_sas

the -q flag and run g_sas again, seg fault again. After searching, I did this: source /usr/local/gromacs/bin/GMXRC Then g_sas worked fine( without the -q flag). But I've already sourced GMXRC.bash. Any clue? Terry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Strange behavior from g_sas

inconsistent shifts lines which I ignored before. I still don't understand why g_sas can work with the first three trjs but the last one in the same for loop. Terry On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 30/03/2011 5:58 PM, Terry wrote: Hi, all, I

Re: [gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

128 After insertion, there are probably several DPPC molecules removed. Check outputs from inflategro.pl, then update accordingly. Terry

Re: [gmx-users] box size continuing the previous energy minimization

the previous completed energy minimization by increasing nsteps. How can I do this? increase in nsteps, and may be the tolerance too. Actually, you need to start from the output .gro file, and *decrease* the emtol value, if your previous minimization converged. Terry Best wishes Mustafa

Re: [gmx-users] dssp problem

caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. You should issue: export DSSP=/home/m/DSSP See, /home/m/DSSP is actually the /path/to/dssp in your case. Terry And also I

Re: [gmx-users] Optimization of the box size during an energy minimization?

possible? Do you mean energy minimization with pressure coupling? Terry Sure, that's in the manual and covered in tutorials. Mark Is there a workaround if there is no direct way? Thanks! Ting -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Installation GROMACS UBUNTU

file to see what's wrong. I suggest you go to a experienced Linux user for help if you don't want to figure out how configure and make work. Terry On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am

Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following

[gmx-users] No K+ for ffG53a6 ?

Hi all, I am new to gmx. I want to use potassium ions in my system. But grompp gives me only error. So I go through ffG53a6.atp, but find no atom type for potassium. Is this normal or I made some mistakes? If this is normal, how can I use potassium ion with ffG53a6? Thanks Terry -- gmx-users

Re: [gmx-users] amber force field in gromacs

Hi, Sorry for my mistake before, column 17 should be alternative location code, not blank. Good luck Terry 2009/11/21 leila karami karami.lei...@gmail.com Hi I used amber03 force field in gromacs to study pr-dna interaction. I compare my pdb file and ffamber03.rtp file. I should correct

Re: [gmx-users] grompp error! why?

. The error is: Error 0 [file unk.itp,line 4] Not enough parameters ….. Fatal error: Bonded/nonbonded atom type '1' not found! My pro.top file: #include “ffg43a1.itp” Did you input this line with keyboard? Try #include ffG43a1.itp Terry #include “unk.itp” [molecules

[gmx-users] range of magnitude for force constant

manual). Considering the units of k_c, is 500kJ/mol way off? -- Cheers, Terry ___ 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 posting

[gmx-users] Amber port for GROMACS 4.0

? No! The ports are numbered to coincide with GROMACS releases, and minor differences between GROMACS versions render the ports non-interchangable. -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] [ angle_restraints_z ]

? - Are the above parameters (theta/K/multiplicity) reasonable/correct? - with this I should expect a1 and a2 stay in xy-plane (with their z component equal at each frame) during minimization, equilibration and production? Thanks. -- Cheers, Terry Did you look at formula 4.68 in the manual

[gmx-users] [ angle_restraints_z ]

minimization, equilibration and production? Thanks. -- Cheers, Terry ___ 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 posting! Please don't

[gmx-users] viewing .xvg plots in windows environment

Hi, I am trying to view my GROMACS .xvg outputs (2D plots) in windows XP environment. Can anyone please suggest a good way to do this? -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] which tpr?

words, in the above example replacing start.tprwith three.tpr will not change the outcome? Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http