Re: [gmx-users] Fwd: Residue 1 mapping problem?

On 8/22/17 5:28 AM, morpheus wrote: Thanks! Is this also just a note or is there a problem? " WARNING 1 [file md_vsIonDod.mdp]: The sum of the two largest charge group radii (18.373196) is larger than rlist (1.40) " I found this on the gromacs webpage: "A similar error ("The

Re: [gmx-users] Average and bfactors.pdb

On 8/21/17 5:25 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin Thank you so much for replyingAccording to the gromacs tuturial, i am

[gmx-users] g_cluster

Dear All, I am using g_cluster. I am wondering what two groups used for? group 1 for fit and RMSD calculation group 2 for output is g_cluster use RMSD values for clustering based on group 1 or group 2? Any suggestions? Thanks Nikolai -- Gromacs Users mailing list * Please search the

[gmx-users] 2nd CfP: From Virtual Reality to Immersive Analytics in Bioinformatics (SD 2018)

2nd CfP "From Virtual Reality to Immersive Analytics in Bioinformatics" February 2018, Burlingame, California, USA Special Session at the Stereoscopic Displays and Applications XXIX, Burlingame, California Special Issue of the Journal of Integrative Bioinformatics, vol 15, de Gruyter Berlin

Re: [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

Hi Mark, I’ll look in more detail the literature regarding this situation. Thanks a lot for your reply. Best, Carlos -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca,

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

Hi, I don't understand whether you think diglycine is your solvent or your solute. Mark On Tue, Aug 22, 2017 at 8:40 AM Dilip H N wrote: > Hello, > 1] it is the solute+Diglycine which is the constituting the mixture... > 2] the method to create the system for both

Re: [gmx-users] Extract only last frame from a trr

Hi, That functionality would be convenient for you, but hasn't been written. I suggest using gmx check to report on the details of the last frame, and use that to construct input to trjconv. Mark On Tue, Aug 22, 2017 at 4:58 PM CLARK NICOLAS Joan wrote: > Dear gmx

Re: [gmx-users] Regarding indexing the atom labelled same in peptide

Hi, The "1" selects the first index group, which is the whole peptide. If you want to select the first residue, you have to use some other syntax. Mark On Tue, Aug 22, 2017 at 6:50 PM Dilip H N wrote: > Hello, > I have a Diglycine peptide in .gro file as:- > 1GLY

Re: [gmx-users] installation_server machine_error

Hi, Please don't start new work with software that's no longer support and is missing over four years worth of performance and correctness fixes. Some of your problems relate to using commands that use the gmx wrapper binary, which did not emerge until version 5.0. Mark On Wed, Aug 23, 2017 at

Re: [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

Hi, The emails have been arriving, but you're asking a complicated series of questions. You need to find some literature that shows these protein and lipid force fields were parameterized in a compatible way, and even then you may need to show that you in fact get a physically reasonable result.

[gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

Dear gmx users, This is the third time I’m sending this email, but for some reason is not been accepted. I’m trying to set up a system consisting in a protein embebed into a bilayer. The whole system contains approximately ~40 atoms, so to speed up the simulation I'm using virtual sites. I

Re: [gmx-users] Missing values in enery EDR

Hi, Check your log file, where it likely says that energy groups are not supported on GPUs. Do a rerun on your traj you want to compute these things. Mark On Wed, 23 Aug 2017 12:08 Sergio Manzetti wrote: > Hi, when running gmx energy on a simulation ouput, I

[gmx-users] Missing values in enery EDR

Hi, when running gmx energy on a simulation ouput, I get: --- 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential 13 Pres.-DC

Re: [gmx-users] installation_server machine_error

Well it seams that you compiled Gromacs with mpi support so now you should run it with sth. like that: mpirun -np 1 /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx_mpi -f 1aki.pdb -o 1AKI_processed.gro -water spceRun:man mpirunfor more details. On Wednesday, August 23, 2017, 10:42:47 AM GMT+3, Kashif

[gmx-users] installation_server machine_error

dear sir after installing gromacs on server, I could not able to run the simulation. It always shows "-bash: command not found". when I tried to locate the pdb2gmx, it showed the path as- /opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi When I run the following command by using the path as