Re: [gmx-users] Re: g_hydorder

First I created index file with all oxygen atoms of water molecules using make_ndx -f lys_full.gro -o index_soloxy.ndx Then I used g_hydorder -f lys_full.xtc -s lys_full.tpr -n index_soloxy.ndx -or file1.out file2.out Following output appeared: Program g_hydorder, VERSION 4.6.3 Source code file: /

RE: [gmx-users] Regarding lipid bilayer

And apparently you have only 6438 atoms in system_inflated.gro. So that is the source of the error. >-Original Message- >From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >boun...@gromacs.org] On Behalf Of hasthi >Sent: 08 October 2013 05:56 >To: gmx-users@gromacs.org >Subject: [gmx-

[gmx-users] On the usage of g_sas

Hi, I would like to use g_sas to determine the surface properties of an organic molecule and was wondering whether to trust g_sas in picking the hydrophobic/hydrophilic atoms. I also saw one can supply an option index file -f_index) for that but nothing is said about the form of this file. Which

[gmx-users] Question about installing DSSP on Ubuntu 12.10

I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu software centre but when I run it I am getting the following error, any solution? I have checked all the mail list archive and could not solve my problem Fatal error: Failed to execute command: /usr/local/bin/dssp -na

Re: [gmx-users] Can I generate Pulf files after mD running?

On 10/7/13 9:41 PM, Yoochan,Myung wrote: Dear gmx-users, I have just finished umbrella MD but I missed to type pullf/pullx options on mdrun. If you omitted the pull-nstfout and/or pull-nstxout options in the .mdp file, their default values are taken and the files should have been produced.

Re: [gmx-users] On the usage of g_sas

On 10/8/13 7:27 AM, Jernej Zidar wrote: Hi, I would like to use g_sas to determine the surface properties of an organic molecule and was wondering whether to trust g_sas in picking the hydrophobic/hydrophilic atoms. I also saw one can supply an option index file -f_index) for that but nothin

Re: [gmx-users] Question about installing DSSP on Ubuntu 12.10

On 10/8/13 7:28 AM, Mass wrote: I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu software centre but when I run it I am getting the following error, any solution? I have checked all the mail list archive and could not solve my problem Fatal error: Failed to exec

[gmx-users] Re: questions

Dear Dwey, Please direct questions like this to the gromacs user list, after asserting that the answer has not already been given. In addition, please read http://md.chem.rug.nl/~mdcourse/molmod2012/md.html Regards, Tsjerk On Tue, Oct 8, 2013 at 5:35 PM, Dwey wrote: > Dear Tsjerk, > >I s

[gmx-users] Is Gromos force field 45a3 out of dated?

Hello, I submitted a paper and get rejected immediately by editor because of the following comment. "The simulations described here rely on an outdated force field (Gromos 45a3) and I suspect that the partial unfolding described here is at least in part due to force field artifacts. " Our simula

[gmx-users] Iron(III) Chloride in water

I want to simulate Iron(III) Chloride in water (in order to test some iron sequestering agents). I've tried to use acpype to generate an iron ion but it errors. So I used genion and labelled the positive ion "FE" with charge of 3. However grompp does not recognize the atom "FE". My question is h

Re: [gmx-users] Is Gromos force field 45a3 out of dated?

Hi Lin, I would say that it is not correct to call 45a3 deprecated. Like other force fields, GROMOS 45a3 is also the result of careful parameterization. The later GROMOS forcefields 53a5, 53a6, 54a7 and 54a8, took of a completely different approach in parameterization, and are in that respect not

[gmx-users] CHARMM36 force field available for GROMACS

All, I am pleased to announce the immediate availability of the latest CHARMM36 force field in GROMACS format. You can obtain the archive from our lab's website at http://mackerell.umaryland.edu/CHARMM_ff_params.html. The present version contains up-to-date parameters for proteins, nucleic

[gmx-users] Re:On the usage of g_sas

Dear Justin, Thanks for the help. That's what the manual says about the "-f_index" switch: "Determine from a group in the index file what are the hydrophobic atoms rather than from the charge" What confuses me is that this is the only thing related to the matter, no word about the naming conv

Re: [gmx-users] Re:On the usage of g_sas

On 10/8/13 10:39 PM, Jernej Zidar wrote: Dear Justin, Thanks for the help. That's what the manual says about the "-f_index" switch: "Determine from a group in the index file what are the hydrophobic atoms rather than from the charge" Ah, I see now. I misread the initial post. The he