[gmx-users] Dihedral Autocorrelation Function with negative values

Dear gmx users, I am writing to ask why I am getting a dihedral autocorrelation function (ACF) with negative values. I am trying to calculate the ACF using g_angle (gromacs 4.5.5) with the following set of flags: g_angle -f trajectory.xtc -type dihedral -oc acf.xvg -od angdist.xvg -n angle.ndx T

[gmx-users] Funnel Metadynamics using PLUMED/Gromacs

Dear gmx/plumed developers, I know that this is probably a question for the PLUMED mailing list more than the GMX mailing list but considering that the question involves GROMACS as well I thought to post it here first. I have read with great attention the paper by Limongelli et al. published on t

Re: [gmx-users] MARTINI force-field in pulling simulations

Thanks Justin. The help has been much appreciated. Cheers, Davide On 7/02/13 8:46 PM, "Justin Lemkul" wrote: > > >On 2/7/13 2:29 PM, Davide Mercadante wrote: >> Thank you Justin, >> >> I guess this means that this kind of simulations is not possib

Re: [gmx-users] MARTINI force-field in pulling simulations

RTINI uses fixed >secondary structure (bonds in the topology to preserve geometry). You're >probably just pulling against those and the algorithms that work on >bonded >interactions are failing. > >-Justin > >> Thanks. >> >> Davide >> >> On 7/02/1

Re: [gmx-users] MARTINI force-field in pulling simulations

of the whole molecule occurs and I see the force peaking? I am still not sure why this happens... Thanks. Davide On 7/02/13 1:05 PM, "Justin Lemkul" wrote: > > >On 2/7/13 5:20 AM, Davide Mercadante wrote: >> Dear All, >> >> I am trying to run a pulling

[gmx-users] MARTINI force-field in pulling simulations

Dear All, I am trying to run a pulling simulation on a small protein (18 aa) using the GC forcefield MARTINI (v2.2). I have energy minimized and equilibrated (NPT) my system and everything seems fine. My system consists of the protein + water + ions NA+ and CL-. After the equilibration I start a

Re: [gmx-users] GROMACS 4.6 release is ready!

That is really great..Thanks for all the work on this! Cheers, Davide On 21/01/13 9:09 AM, "Mark Abraham" wrote: >Hi GROMACS users, > >The day is finally here - GROMACS 4.6 is out! > >As you've probably heard by now, there are lots of wonderful new >performance features, including >* a native G

Re: [gmx-users] Umbrella sampling - chain A does not get pulled

; wrote: > > >On 12/11/12 2:40 AM, Davide Mercadante wrote: >> Dear Justin, >> >> I have been practicing umbrella sampling simulations following your >>tutorial >> step by step. I have just finished to perform the pull simulations to >> identify

[gmx-users] Umbrella sampling - chain A does not get pulled

Dear Justin, I have been practicing umbrella sampling simulations following your tutorial step by step. I have just finished to perform the pull simulations to identify the configurations to use in the umbrella runs. I have used the distances.pl script to run iteratively g_dist and the resulting f

Re: [gmx-users] Re: Multiple protein simulations in a box

Hi Rajeswari, try this really interesting work done by De Simone et al. and published recently on PNAS. http://www.pnas.org/content/109/18/6951.full Hope this helps. Cheers, Davide Davide Mercadante Ph.D. School of Chemical Sciences The University of Auckland Auckland New Zealand On 3

Re: [gmx-users] remd jobs failed

>thanks for kind reply. >The .tpr file was created by grompp in cluster and there is no problem >for that. > >thank you very much >Albert > >On 10/19/2012 08:52 AM, Davide Mercadante wrote: >> Hello, >> >> Basically is telling you that the output (.tpr) file

Re: [gmx-users] remd jobs failed

Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, "Albert"

[gmx-users] How to create a gmx topology for a polysaccharide using glycam 06?

Dear gmx users, please accept my apologies if mine is a stupid question or it has already been done to you. I have been looking at the mailing list but I was unable to find any satsfying answer to my problem. I am going to run MD on a homogalacturonan chain (polysaccharide like chain composed by a

Re: [gmx-users] Segmentation Fault using g_cluster

Wed, 28 Mar 2012 13:29:40 +1100 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Segmentation Fault using g_cluster On 28/03/2012 1:00 PM, Davide Mercadante wrote: > > Dear Gromacs Users, > > > > > I am trying to run g_cluster to find an avera

[gmx-users] Segmentation Fault using g_cluster

Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n ­g g_cluster started without problems and continued calculating the matrix etcŠuntil I g

Re: [gmx-users] RMSD sudden jump

Sorry I realized I attached the .xvg. Here is a png for a easier visualization. Sorry for the inconvenience. Thanks, Davide 2012/3/14 Davide Mercadante > Hi Tsjerk, > > thanks very much for your prompt reply. > I checked the last 5ns rmsd against an average structure calculated i

Re: [gmx-users] RMSD sudden jump

nce structure, the > molecule undergoes a transition to another state. To see if it > converges in that state in the time of your simulations, get the > average structure from the last 5 ns of the simulation and run the > RMSD against that. > > Cheers, > > Tsjerk > >

[gmx-users] RMSD sudden jump

ou! Davide -- Davide Mercadante - PhD student - School of Chemical Sciences The University of Auckland 1142 Auckland, New Zealand <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppo