[gmx-users] H-bond calculation

Dear gmx, I would like to calculate the H-bond occupancy between two residue (intra mol inter Thr183 (OG1) -Tyr162 (N) ). I made a .ndx file choosing the both atoms : Group40 ( r_162_&_N) has 1 elements Group

Re: [gmx-users] Fixing periodicity effects on trajectory file

Dear Justin ​If you asked about verifying docking process​. I should say, I have worked with single chain protein and the best ranked binding energy was -7.41 kcal/mol by AutoDock 4.2, considering that binding site was located on turn structure and the edge of protein, seeming unstable. I didn't ch

Re: [gmx-users] Atomic charges

Which force field are you using? How did you obtain the charges? OPLSAA has its own charges., which can be modified for new molecules. Chandan On Wed, Sep 16, 2015 at 9:57 AM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello users, > > I have this confusion regarding the a

[gmx-users] Atomic charges

Hello users, I have this confusion regarding the atomic charges that gromacs sees. I have defined my residues in aminoacids.rtp file with my own charges, but the atom types for the same in the ffnonbonded.itp have different charges on them. Which of the two charges would Gromacs pick? Thank you.

Re: [gmx-users] miscelle formation using ligands only

so what is the best option for topologies. On Wed, Sep 16, 2015 at 2:19 AM, Justin Lemkul wrote: > > > On 9/15/15 11:35 AM, Chetan Puri wrote: > >> thanks for you help and today i was able to solve the problem, >> actually my pdb file was made using packmole for 5 molecules and molecules >> wer

Re: [gmx-users] Fixing periodicity effects on trajectory file

Maybe the ligand actually is leaving the binding site and moving around, and that's what your simulation is telling you! Hard to say with the posted information. On Tue, Sep 15, 2015 at 11:24 AM, Homa rooz wrote: > Dear Justin > I have followed your advice but it didn't solve my problem. > Ligan

[gmx-users] Problem with wall!

Dear all, I am a new gromacs user. I want to simulate a box with two charged walls contain water molecules, but i face to many problems! for example water molecules go out of box. Could anyone help me by explain details of wall simulation? thanks in advance. -- Gromacs Users mailing list * Plea

[gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

Hello. I want to use a dynamic selection scheme (select different atoms based on the same selection criteria for each frame of a trajectory) and pass this selection/ info to the gmx dipoles tool. It seems that the -select option cannot be used. I tried to use dynamic selection through gmx select. T

[gmx-users] Efficiently running multiple simulations

Hello, I am having some troubles efficiently running simulations in parallel on a gpu-cluster. The cluster has 8 GPUs and 16 CPUs. Currently, the command that I am using is: mpirun -np 8 mdrun_mpi -multi 8 -nice 4 -s md -o md -c after_md -v -x frame -pin on Per-simulation, the performance

Re: [gmx-users] Fixing periodicity effects on trajectory file

On 9/15/15 1:24 PM, Homa rooz wrote: Dear Justin I have followed your advice but it didn't solve my problem. ​Ligand is still out of binding site. Can you verify that it actually did start in the binding site? Was everything built correctly? If so, there's no reason that simply centering

Re: [gmx-users] miscelle formation using ligands only

On 9/15/15 11:35 AM, Chetan Puri wrote: thanks for you help and today i was able to solve the problem, actually my pdb file was made using packmole for 5 molecules and molecules were prepared using prodrug , so my pdb file contained names of DRG A, B,C,D,E PRODRG produces notoriously bad para

Re: [gmx-users] Fixing periodicity effects on trajectory file

Dear Justin I have followed your advice but it didn't solve my problem. ​Ligand is still out of binding site. -- Homa Ahmadi Shahed University Faculty of Basic Sciences Alternative email> h.ahm...@shahed.ac.ir -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] miscelle formation using ligands only

thanks for you help and today i was able to solve the problem, actually my pdb file was made using packmole for 5 molecules and molecules were prepared using prodrug , so my pdb file contained names of DRG A, B,C,D,E and i tried to change it to SC3,CA1,D3G,. in the last packed PDB file and

Re: [gmx-users] how to install GROMOS 43a1p force field in gromacs 4.5.5 version

On 9/15/15 11:26 AM, rajan kumar choudhary wrote: Dear all please guide me how to install a new force field GROMOS 43a1p thank you all in adavan

Re: [gmx-users] Accelerating data analysis.

Dear Krzysztof, do you convert *trr to *xtc after your simulation or do you write data to the latter one as it proceeds? Dawid 2015-09-15 15:57 GMT+01:00 Krzysztof Kuczera : > Since most of my analyses deal with the protein part, I typically use > trjconv to make an .xtc trajectory with protein

[gmx-users] how to install GROMOS 43a1p force field in gromacs 4.5.5 version

Dear all please guide me how to install a new force field GROMOS 43a1p thank you all in adavance -- *Rajan kumar choudhary* *Senior Research Fellow

Re: [gmx-users] Accelerating data analysis.

Since most of my analyses deal with the protein part, I typically use trjconv to make an .xtc trajectory with protein coordinates only. Running most analyses on that file is at least 10x faster than on whole .trr Krzysztof On 9/15/15 7:42 AM, Erik Marklund wrote: Dear Dawid, The best thing I

Re: [gmx-users] Accelerating data analysis.

Well not necessarily, but it depends on how badly you want to avoid it. Your command line with g_rms -tu us -b ... seemed correct, and it seems to be skipping frames just like you instructed it to. Erik > On 15 Sep 2015, at 14:35, Dawid das wrote: > > Thank you again. So after all I still nee

Re: [gmx-users] Using TIP4P(2005) with GROMOS-53a6

Thank you people. I'll take note of all these points before moving ahead. -Pallavi. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (

Re: [gmx-users] Accelerating data analysis.

Thank you again. So after all I still need trjconv. 2015-09-15 14:24 GMT+01:00 Mark Abraham : > Hi, > > Yes. There is no intelligence about .trr reading (unlike .xtc) so it reads > every frame until one that satisfies your constraint. You will have a > better time implementing Erik's strategy if

Re: [gmx-users] Accelerating data analysis.

Hi, Yes. There is no intelligence about .trr reading (unlike .xtc) so it reads every frame until one that satisfies your constraint. You will have a better time implementing Erik's strategy if you break the trajectory into parts with trjconv, convert it to .xtc, or write it as .xtc in the first pl

Re: [gmx-users] Accelerating data analysis.

Something is wrong here. I use following command: g_rms -tu us -b 0.9 -e 1.0 -s npt-md2.tpr -f npt-md2.trr -n index.ndx -o rmsd-protein.xvg and g_rmsd still starts from 0 and it says "Skipping frame..." and it seems it will skip all frames (as it would read it) until 0.9 us. Is that what I should

Re: [gmx-users] Accelerating data analysis.

Dear All, Thank you all. Especially for your tip Erik ;). Dawid 2015-09-15 13:42 GMT+01:00 Erik Marklund : > Dear Dawid, > > The best thing I can think of is to analyse different parts of the > trajectory in parallel, using separate g_rms processes, then concatenating > the output. Use -b and -

Re: [gmx-users] Accelerating data analysis.

Dear Dawid, The best thing I can think of is to analyse different parts of the trajectory in parallel, using separate g_rms processes, then concatenating the output. Use -b and -e options to limit the analysis to specific intervals. Kind regards, Erik > On 15 Sep 2015, at 13:37, Dawid das wro

Re: [gmx-users] Accelerating data analysis.

On 9/15/15 8:37 AM, Dawid das wrote: Dear Gromacs Experts, I have an enormous *trr file, which has 1 000 000 points. Now, I know that I can modify this file with trjconv, but let's say I do not want to do it, but I want to have my 1 000 000 points in *xvg file when I use g_rms for instance. Is

[gmx-users] Accelerating data analysis.

Dear Gromacs Experts, I have an enormous *trr file, which has 1 000 000 points. Now, I know that I can modify this file with trjconv, but let's say I do not want to do it, but I want to have my 1 000 000 points in *xvg file when I use g_rms for instance. Is there a way to accelarate it? Best wish

Re: [gmx-users] Fixing periodicity effects on trajectory file

On 9/15/15 7:39 AM, Homa rooz wrote: Hi there I'm working with gromacs for ligand-protein interaction simulation. I have run MD for docked complex and now there is a problem with trajectory visualization by VMD. The ligand has left binding site circulating around the protein. I tried to fix the

[gmx-users] Fixing periodicity effects on trajectory file

Hi there I'm working with gromacs for ligand-protein interaction simulation. I have run MD for docked complex and now there is a problem with trajectory visualization by VMD. The ligand has left binding site circulating around the protein. I tried to fix the problem by making index and extract the