RE: [gmx-users] Adding_topology_aminoacid

Dependent on the force field you are using, the topology of free amino acids may not be defined. Look at the content of the rtp-file for your forcefield, if the free amino acid is defined there, you can use pdb2gmx to generate the topology. Otherwise you have to treat the amino acid as a new mo

[gmx-users] -dt option in g_velacc

Hi, gmx users: when I used g_velacc to calculate VAF, I found the minimum of dt could be taken to 0.1 ps, but smaller. If I want to gain more precise results, how can I do?? thanks! -- Sincerely yours Dr Ji-Nan Niu School of Materials Science and Engineering. China University of Mining a

Re: [gmx-users] -dt option in g_velacc

On 8/08/2011 6:28 PM, Jinan Niu wrote: Hi, gmx users: when I used g_velacc to calculate VAF, I found the minimum of dt could be taken to 0.1 ps, but smaller. If I want to gain more precise results, how can I do?? I don't quite follow your question, but for correlation functions to be comput

[gmx-users] Re: Carbon Nanotubes with Cisplatin Inside it

Please post all Gromacs-related correspondence to the gmx-users list. I am not a private tutor. I am CC'ing this message to the list as it may be of interest to others. My comments are embedded below. meisam valizadeh kiamahalleh wrote: Dear Justin Good day to you I would like to create a

[gmx-users] Re: Essential Dynamic analysis

As I said in my previous message, please post all Gromacs-related correspondence to the gmx-users list. I am not a private tutor. I am CC'ing this message to the list and ask that all further discussion be posted there. ED (or PCA) is a post-processing analysis procedure. There are details

Re: [gmx-users] Re: Essential Dynamic analysis

Hey Fatemeh, Maybe the section on PCA at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html is of any use... Cheers, Tsjerk On Mon, Aug 8, 2011 at 2:27 PM, Justin A. Lemkul wrote: > > As I said in my previous message, please post all Gromacs-related > correspondence to the gmx-users li

[gmx-users] Regarding PCA and FEL

Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-user

[gmx-users] Conversion of the GLYCAM dihedral parameters

> > Thank you Olivier for your response. > SA > -- > > Message: 2 > Date: Thu, 28 Jul 2011 11:20:44 +0100 > From: Oliver Grant > Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > To: Discussion list for GROMACS users > Message-ID: > >

[gmx-users] Restart a simulation from a power source failure

Hi all, I'm trying to restart a simulation from a power source failure, but mdrun complains about a missing .trr file: Program mdrun, VERSION 4.0.7 > Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737 > > Can not open file: > traj.trr > > The manual says that there is no need to supply

Re: [gmx-users] Restart a simulation from a power source failure

Luís Pereira wrote: Hi all, I'm trying to restart a simulation from a power source failure, but mdrun complains about a missing .trr file: Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737 Can not open file: traj.trr The manual says

Re: [gmx-users] Restart a simulation from a power source failure

Hi Justin, Thank you for your quick answer. All the files are in the working directory but have different names, e.g., the .trr is not traj.trr but 7fboh3.trr, and so on. I've backed up the working directory, run gromacs with all output file names written in command line and now everything is work

Re: [gmx-users] Restart a simulation from a power source failure

Luís Pereira wrote: Hi Justin, Thank you for your quick answer. All the files are in the working directory but have different names, e.g., the .trr is not traj.trr but 7fboh3.trr, and so on. If you do not supply filenames, then the defaults are assumed. This is true of all Gromacs program

[gmx-users] (no subject)

I'm trying to install gromacs-3.3 & am constantly getting errors regarding configure: error: C++ preprocessor "/lib/cpp" fails sanity check or CC non executable. Is this because my version of Linux is too new because these errors were not happening when I installed the newest versions of Gromacs?

[gmx-users] Free energy calculation

Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution --> drug with only vdW in solution --> dummy drug in solution). After reading most of the papers, I understand that you need significant overlap from the energies for each intermediate point to overlap so

Re: [gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute

I was dealing with the same situation. I am using the latest version of DSSP (April 2011). Neither gromacs 4.5.3 or 4.5.4 would work. After applying Pradip's patch, do_dssp worked for me. I would say that the change in flags is related to the fact that "In 2011 Maarten Hekkelman has written new so

Re: [gmx-users] (no subject)

Janowicz, Adrianna C. wrote: I'm trying to install gromacs-3.3 & am constantly getting errors regarding configure: error: C++ preprocessor "/lib/cpp" fails sanity check or CC non executable. Is this because my version of Linux is too new because these errors were not happening when I installed

Re: [gmx-users] Free energy calculation

Fabian Casteblanco wrote: Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution --> drug with only vdW in solution --> dummy drug in solution). After reading most of the papers, I understand that you need significant overlap from the energies for each in

[gmx-users] Regarding PCA and Free energy landscape

Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users