[gmx-users] rvdw and DispCorr

Dear gromacs users In a recent paper I found the following protocol of a gromacs simulation: All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the

[gmx-users] do_dssp

Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied it to the correct location: cp dssp-2-linux-i386 /usr/local/bin/dssp and gave the user the right to

[gmx-users] Re: gmx-users Digest, Vol 96, Issue 30

Am 04.04.2012 14:03, schrieb gmx-users-requ...@gromacs.org: Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp fromhttp://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied

[gmx-users] Question regarding tpr files and rmsd

Dear users Due to a hard disk crash we lost several md simulations. Fortunalty we have backup copies of the trajectry files (xtc format) and structure files of the first frame of the simulation (created via trjconv -b 0 -e 0 -f myName.md.trr -o myName.md.firstframe.pdb -s myName.md.tpr).

[gmx-users] Re: Re: problems with some calculated trajectories

1) trjconv with the -pbc nojump option does not help - it removes most of the jumps but one big remains- the rmsd for the trajectory is http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg before the converting with -pbc and http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg after conversion.

[gmx-users] Re: Re: Re: Re: problems with some calculated trajectories

The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope, T-cell receptor alpa, T-cell receptor beta). What you can see in http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg is exactly the same angle. The

[gmx-users] problems with some calculated trajectories

Dear users I performed some long-time simulations using gromacs 4.0. The longest simulation trajectory is about 62 ns. Unfortunately the trajectory seems to be damaged. If I calculate the RMSD of different interesting regions the values are beginning to jump up an down after about 17 ns in

[gmx-users] hardware recommendation

Dear users Are there any hardware preferences for using Gromacs with best performance? The ones from the Gromacs FAQ seem quite out dated to me. So which hardware infrastructure would you buy with 35k euro? cheers Bernhard ___ gmx-users mailing

[gmx-users] Gromacs and ssh problem

Hi I installed Gromacs successfully on Fedora 8 nodes. Afterwards I ran a successful small simulation. Thereafter I moved the node to our server-room did the following: - set ip adress, subnetmask and gateway - changed the ssh port in /etc/ssh/sshd_config since we use port forwarding on our

[gmx-users] Re: Gromacs 4 bug?

If someone is interested: Finally our nodes are working fine using Fedora Core 8, fftw-3.1.3, openmpi-1.3 and gromacs-4.0.3. Thank you very much for your time and effort! cheers Bernhard Message: 2 Date: Thu, 15 Jan 2009 08:37:16 +0100 From: patrick fuchs

Re: RE: Re: Re: [gmx-users] Gromacs 4 bug?

Hi Berk, I continued the simulation and it works fine (for the next few hours). Then it gets stuck again. So it seems that the problem is not directly related to gromacs. But it seems the interaction between the operating system or the hardware does not work for a longer time. We are using

[gmx-users] Gromacs 4 bug?

Dear users I have a problem with gromacs 4 (also tried 4.0.2). If I start a simulation it is calculating for some time but after about one day it gets somehow stuck. This means that the simulation is still running and the top commands says md still uses all 4 cores of the computer: 5487

Subject: Re: Re: [gmx-users] Gromacs 4 bug?

Mark wrote: What's happening in the log files? What's the latest information in the checkpoint files? Could there be some issue with file system availability? Hi Mark Unfortunaltey I already deleted the simulation files which got stuck after 847ps. But here is the output of another

[gmx-users] Re:Re: x2top

Justin wrote: It looks like your coordinate file is from PRODRG; why not use PRODRG to generate a rough topology, and refine it according to the ffG43a1 parameters? The problem is that the sugar in in contact with a bigger protein complex and the PRODRG server is not willing to accept

[gmx-users] x2top

Dear Users I tried to use the x2top function of gromacs 4 on a sugar-molecule. But the gromacs says that it requests the ffgmx.n2t library which can not be found in the default directory. I searched in the whole system but could not find it. Therefore I also searched on an other system with

[gmx-users] sedoheptulose

Dear users I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via Gromacs. But already during pdb2gmx it comes up with: Residue 'UNK' not found in residue topology database which is obviously clear since sedoheptulose is not an amino acid. Is it somehow possible to simulate

Re: RE: [gmx-users] sedoheptulose

://wiki.gromacs.org/index.php/FAQs x2top and the prodgr web-server might be some good starting points. Andreas From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Knapp Sent: 19 November 2008 12:54 To: gmx-users@gromacs.org Subject: [gmx-users] sedoheptulose Dear users I

[gmx-users] gromacs 4.0 release

hi is there any new information on the release of gromacs 4? currently we are planning to install gromacs on a new cluster and we are not sure if it is worth to install the old 3.3 version or to wait for the 4.0 release? thx Bernhard -- Bernhard Knapp Unit for Medical Statistics

[gmx-users] acetyl

Hi there, I wanted to ask if gromacs is able to deal correctly with peptides which have been acetylized at the N-terminal end? if so what would be the approbriate way (tool) to model the acetyl? thx Bernhard -- Bernhard Knapp Unit for Medical Statistics and Informatics - Section