[gmx-users] Ligand and ion topology

Dear gromacs users, I have a protein with GNP ligand and acetate ACT ion that I want to simulate. I have prepared topologies for both GNP and ACT with PRODRG program. My first question is: Where should I exactly include the ACT.itp and GNP.itp into topol.top file? My second question is: I have

Re: [gmx-users] error in nvidia cuda installation

Dear Stephane, I tried to install drivers and cuda as was syggested in the link you sent me yesterday. I go through the first steps, but after choosing to install cuda and replying yes to all the questions, I got an error indicating that drivers installation failed. What should I do now? Thanks

[gmx-users] topology file with virtual site for an asymetric linear molecule

Dear all, I would like to use the virtual site capability of GROMACS to construct the topology of an asymmetric linear molecule (say SeCN). Does somebody have an example of topology file for a similar molecule to share with me? Thank you Stéphane -- Gromacs Users mailing list * Please sear

[gmx-users] Has omega -180 also in proteins?

Dear gromacs users, I have done simulation for 100ns and I analyzed many properties as part of my work. I also calculated the omega dihedral angle and I got the values around +180 and -180 degrees. When I present the work in lab they questioned about the omega values of PROLINE. It should be ar

Re: [gmx-users] error in nvidia cuda installation

Dear Stephane, I followed the instructions in this link: http://www.steletch.org/spip.php?article89 With ctrl+alt+f1 I went to console, then I logged in and typed: sudo service lightdm stop there was an error : Unit lightdm.service not loaded Then I typed: sudo rmmmod nvidia I got another error

Re: [gmx-users] error in nvidia cuda installation

Hi, from terminal go sudo init 3 it will take you to the screen where you can install all this drivers and cuda tool kit.. then come out with sudo init 5 and reboot. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Has omega -180 also in proteins?

Dear Surya, I think -180 and 180 degrees are equivalent, i.e. 181 should be represented as -179 and -181 as +179. Best regards, Andras Wacha On 07/04/2017 02:11 PM, Seera Suryanarayana wrote: > Dear gromacs users, > I have done simulation for 100ns and I analyzed many properties as part of > m

Re: [gmx-users] error in nvidia cuda installation

You have to close all X window, disconnect, then go to the console using ctrl+alt+F1, an then: 1) turn off the xserver and/or the login manager: sudo service lightdm stop (in Ubuntu) sudo service gdm stop (Mint) 2) performs the steps again, it should work now 3) reboot (the initrd/initramfs

Re: [gmx-users] Ligand and ion topology

Can anyone help, please? *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 On Tue, Jul 4, 2017 at 12:33 PM, Khadija Amine wrote: > Dear gromacs users, > > I have a protein with GNP ligand and acetate ACT ion that I want to > simulate. > > I have prepared t

[gmx-users] Hardware for GROMACS

Hello, I am new to GROMACS and want to assemble a computer to run simulations of proteins and polymers (typically <50 kD). My questions are: 1. I plan to add two or three small-sized GPUs (768 CUDA cores/GPU) to the system. Is it OK to have a dual core processor or should I look for a processo

[gmx-users] methylated HSP

Hi, I am going to simulate a protein with a methylated histidine in Gromacs using CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in pdf file. I have followed the discussion in https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=15364&page=all but I c

[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

Dear GROMACS Users, I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI. I want to include 0.150 M KCl in the system. When I use the option in charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the number of ions using the size of simulation box, I am ge

Re: [gmx-users] error in nvidia cuda installation

Thanks a lot Stephane and Nikhil Regards, Neda - Original Message - From: Stephane TELETCHEA To: gromacs org gmx-users Sent: Tue, 04 Jul 2017 18:47:56 +0430 (IRDT) Subject: Re: [gmx-users] error in nvidia cuda installation You have to close all X window, disconnect, then go to the con

[gmx-users] Automake problem during installation 4.5.7

Dear all, I am trying to install 4.5.7 (because I need to use a forcefield which is for 4.5.X) with MPI on our system here which runs Scientific Linux 6.3. I managed to do some SETENV to get the library and include paths set up, and configure finished without issues. But when I tried to do "make

Re: [gmx-users] Can not open file: run.trr

Thank you On Mon, Jul 3, 2017 at 5:36 AM, Mark Abraham wrote: > Hi, > > Use tools like rsync to do your file copies and preserve suitable > permissions automatically. And try to avoid copying files > 2GB to > partitions formatted in Windows-friendly fashion to e.g. FAT32 file sytems, > as extern

Re: [gmx-users] methylated HSP

pdf attached now. --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@

Re: [gmx-users] methylated HSP

Ok attachment was not a good idea, atomtypes are in this mail. [ HIC ] [ atoms ] N NH1 -0.47 0 HN H 0.311 CA CT1 0.072 HA HB1 0.093 CB CT2 -0.05 4 HB1 HA2 0.095 HB2