Re: [gmx-users] performance issue with many short MD runs

Hi, As Peter notes, there are cases where the GPU won't be used for the rerun (specifically, when you request more than one energy group, for which it would likely be prohibitively slow, even if we'd write and run such a kernel on the GPU; but that is not the case here). The reason things take a

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

On 3/26/17 9:40 PM, Dan Gil wrote: Hi, I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on calculating free energy of solvation. Is it possible and theoretically sound to use the md integrator instead of the sd integrator for these calculations? Langevin dynamics gives

Re: [gmx-users] forcefield installation on GROMACS 5.1.4

On 3/27/17 7:44 AM, Simon Kit Sang Chu wrote: Hi everyone, Recently I am looking into PACE for my system and installation of forcefield is required. The files located inside the forcefield directory is given by - aminoacids.rtp cgWater.itp

Re: [gmx-users] Secondary structure analysis

On 3/27/17 6:48 AM, RAHUL SURESH wrote: i found a lot libraries missing in dssp. can i obtain them using *rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/oem/Downloads/dssp* The dssp binary is all you should need. It's pre-compiled (though you can get the

Re: [gmx-users] Extracting Energy of Individual Molecules From Energy File

On 3/27/17 9:20 AM, Kelechi Okoroafor wrote: Hello, All. Please is it possible to extract the different components of energy (i.e. Bond, Angle, Coulombic and LJ) for individual molecule from the *.edr file? Not from the .edr file, but if you extract the coordinates of that molecule from

Re: [gmx-users] solvate with hexagonal box

Hi, Sounds like there is something worth improving, although I can't answer your questions right now. Please open an issue on https://redmine.gromacs.org and attach a tarball of suitable inputs for the two(?) cases. Mark On Mon, 27 Mar 2017 13:54 Erik Marklund wrote:

Re: [gmx-users] calculation of self energy of protein

On 3/27/17 2:02 AM, Saumyak Mukherjee wrote: Dear Justin, Is there any way to get just the interaction energy between protein and water? In this case, the energy should not contain the self or inherent energy. Set the protein and water as separate energygrps and extract the relevant

Re: [gmx-users] Protein preparation

On 3/27/17 2:16 AM, Rasika Kelum wrote: Thank you Justin. Highly appreciate your help. If there are missing residues, any suggestions on fixing the protein? There are plenty of tools to do that; Modeller is one of them. 1. How to find correct sequence? (is there any website to find

Re: [gmx-users] Regarding Glycine structure

On 3/27/17 8:50 AM, Dilip H N wrote: Thanks Justin, But my doubts are.. 1] after energy minimization of both glycine non zwitterionic form and zwitterionic form with water, if i visualize it in vmd, the bond between some of the water molecules are broken.. why is this so..??

Re: [gmx-users] Restraining Protein-ligand distance

On 3/27/17 8:42 AM, Juan José Galano Frutos wrote: Hi there, I am trying AFEC simulations in complex (ligand-protein), but sometimes I get the ligands out the binding site, but I dont want that scenary. I was thinking the situation of applying distance retraints between a ligand and a protein

Re: [gmx-users] Unbiased or biased

On 3/27/17 11:02 AM, m g wrote: Dear Justin Lemkul,I red your tutorial "Umbrella Sampling", I want to know about unbiased and biased method. you sad that used biasing potential. which parameter in md files refers to biased? how can i used unbiased method? what An applied external potential

[gmx-users] topology

What if I run my protein-ligand simulation with out using *; Include ligand topology #include "drug.itp"* in the topology file generated using pdb2gmx. but i have added my ligand in protein.gro file. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* --

[gmx-users] Is My NPT Density High?

Hello all, I have a system with a protein, lipid bilayer, and water/ions. I am getting a density of 1034 kg/m^3. I would have expected it to be lower because of the lipids. Is this a reasonable density for such a system? Image of system: http://oi64.tinypic.com/35jaykl.jpg NPT_density.xvg:

Re: [gmx-users] Regarding Glycine structure

i want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW, etc., So my commands were as follows... 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx > del 2 Removed group 2 'SOL' > del 1 Removed group 1 'Water' > del 0 Removed group 0 'System' > a H1 H2 H3 OW Found xxx

[gmx-users] Help in a thermalization

When I tried to do a thermalization for a PSB molecule (it has 66 atoms), in vacuum, the molecule rotate around the center of mass. This's my .mdp file: --- cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50

[gmx-users] protein-ligand

In protein-ligand simulation using charmm36ff, how to generate gro file for ligand to add it to the protein gro file? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Gromacs and Radeon Nano

Hi, after some suggestions and some dealing with AMD I still don't have the working solution. Even I don't have any clue for those freezes/crashes. The double GPU was really mesa and amd driver double checks. I have tried Ubuntu in 14.4.2, 16.4.1 and 16.4.4 versions (first two should be supported

[gmx-users] PMF - US histograms problem

Hi everyone, I'm trying to calculate the PMF for the extraction of a peptide from within a peptide nanostructure. However I'm having difficulty to overlap the histograms for the first pulling windows: Many full overlap windows follow by a large gap with no histogram. I've tried the two things I

Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

Hi They have a web site and all of things you need is there: http://rashmikumari.github.io/g_mmpbsa/ On Mar 27, 2017 10:15 AM, "Neha Gupta" wrote: > Hi gromacs users, > > How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of > amber software

Re: [gmx-users] calculation of self energy of protein

Dear Justin, Is there any way to get just the interaction energy between protein and water? In this case, the energy should not contain the self or inherent energy. Thanks & regards, Saumyak On 27 March 2017 at 11:27, Saumyak Mukherjee wrote: > Thank you very

Re: [gmx-users] Protein preparation

Thank you Justin. Highly appreciate your help. If there are missing residues, any suggestions on fixing the protein? 1. How to find correct sequence? (is there any website to find correct sequence?) 2. How to FIX the sequence (using what software?) 3. Once residues are fixed how would that

Re: [gmx-users] Secondary structure analysis

i found a lot libraries missing in dssp. can i obtain them using *rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/oem/Downloads/dssp* On Sun, Mar 26, 2017 at 9:44 PM, Souparno Adhikary wrote: > I think dssp is a useful tool for this

[gmx-users] forcefield installation on GROMACS 5.1.4

Hi everyone, Recently I am looking into PACE for my system and installation of forcefield is required. The files located inside the forcefield directory is given by - aminoacids.rtp cgWater.itp ffPACE_1.3-c.tdb ffPACE_1.3.hdb ffPACE_1.3-n.tdb

[gmx-users] solvate with hexagonal box

Dear gmx-users, We are trying to merge a box containing a peripheral membrane protein with another box generated with memgen. Both boxes are hexagonal and exactly the same size,Naively, we thought that gmx solvate -cp protein.gro -cs membrane_and_water.gro would do the trick. Unfortunately,

Re: [gmx-users] topology

On 3/27/17 3:23 PM, RAHUL SURESH wrote: What if I run my protein-ligand simulation with out using *; Include ligand topology #include "drug.itp"* in the topology file generated using pdb2gmx. but i have added my ligand in protein.gro file. Then you'll get a fatal error from grompp about

Re: [gmx-users] Regarding Glycine structure

On 3/27/17 3:55 PM, Dilip H N wrote: i want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW, etc., So my commands were as follows... 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx del 2 Removed group 2 'SOL' > del 1 Removed group 1 'Water' > del 0 Removed

Re: [gmx-users] Help in a thermalization

On 3/27/17 4:50 PM, Graziele Bortolini wrote: I do it too, my .mdp file now is like : - cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 comm-mode = angular nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50 nstxtcout = 50 energygrps = PSB nstlist = 10 ns_type = grid

Re: [gmx-users] Help in a thermalization

The error 3 was solved, but when I change to cutoff-scheme = group, I receive: "Fatal error: The largest charge group contains 66 atoms. The maximum is 32." I've tried to make this before, and I saw your answer about this error in this link:

Re: [gmx-users] Help in a thermalization

I do it too, my .mdp file now is like : - cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 comm-mode = angular nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50 nstxtcout = 50 energygrps = PSB nstlist = 10 ns_type = grid rlist = 0 coulombtype = Cut-off optimize_fft = yes

Re: [gmx-users] Is My NPT Density High?

On 3/27/17 3:28 PM, Jonathan Saboury wrote: Hello all, I have a system with a protein, lipid bilayer, and water/ions. I am getting a density of 1034 kg/m^3. I would have expected it to be lower because of the lipids. Is this a reasonable density for such a system? An overall density of

Re: [gmx-users] Help in a thermalization

On 3/27/17 4:12 PM, Graziele Bortolini wrote: When I tried to do a thermalization for a PSB molecule (it has 66 atoms), in vacuum, the molecule rotate around the center of mass. This's my .mdp file: --- cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1

Re: [gmx-users] protein-ligand

On 3/27/17 4:02 PM, RAHUL SURESH wrote: In protein-ligand simulation using charmm36ff, how to generate gro file for ligand to add it to the protein gro file? You don't strictly need a .gro file, since GROMACS can handle PDB and other formats, but in short, you can convert between formats

Re: [gmx-users] performance issue with many short MD runs

Hi, On the new machine your CUDA runtime and driver versions are lower than on the old machine. Maybe that could explain it? (is the GPU even used with -rerun?) You would need to recompile gromacs. Peter On 27-03-17 15:51, Michael Brunsteiner wrote: > Hi,I have to run a lot (many thousands)

[gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

- Forwarded message from sp...@iacs.res.in -    Date: Fri, 24 Mar 2017 16:24:21 +0530    From: sp...@iacs.res.in Subject: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?      To: gmx-us...@gromacs.org Hello, I am a new user of gromacs. I am

[gmx-users] Extracting Energy of Individual Molecules From Energy File

Hello, All. Please is it possible to extract the different components of energy (i.e. Bond, Angle, Coulombic and LJ) for individual molecule from the *.edr file? -- Best wishes, Kelechi -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Restraining Protein-ligand distance

Hi there, I am trying AFEC simulations in complex (ligand-protein), but sometimes I get the ligands out the binding site, but I dont want that scenary. I was thinking the situation of applying distance retraints between a ligand and a protein was already solved in GROMACS version later 5.0...

Re: [gmx-users] Regarding Glycine structure

Thanks Justin, But my doubts are.. 1] after energy minimization of both glycine non zwitterionic form and zwitterionic form with water, if i visualize it in vmd, the bond between some of the water molecules are broken.. why is this so..?? 2] and ran nvt,npt,md simulations respectively...and

Re: [gmx-users] PMF - US histograms problem

Hi, When I get a region sparsely populated like that, I increase the number of points in that particular region and increase the k value to about 3000 but not more than that. Increasing the k value to something like 2 will result in the distribution getting very narrow and therefore further

Re: [gmx-users] Regarding Glycine structure

Sorry it was a typing mistake..it is actually 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx > del 2 Removed group 2 'SOL' > del 1 Removed group 1 'Water' > del 0 Removed group 0 'System' > a H1 H2 H3 OW Found xxx atoms with name H1 H2 H3 OW 0 H1 H2 H3 OW : xxx atoms > q 2]Then,

Re: [gmx-users] protein-ligand

How will I add ligand .gro file in protein .gro file to make a complex .? On Tue, 28 Mar 2017 at 2:12 AM, Justin Lemkul wrote: > > > On 3/27/17 4:02 PM, RAHUL SURESH wrote: > > In protein-ligand simulation using charmm36ff, how to generate gro file > for > > ligand to add it to

Re: [gmx-users] topology

So it is mandatory to add > *; Include ligand topology > #include "drug.itp"* In top file.? On Tue, 28 Mar 2017 at 2:08 AM, Justin Lemkul wrote: > > > On 3/27/17 3:23 PM, RAHUL SURESH wrote: > > What if I run my protein-ligand simulation with out using > > > > > > > in the

[gmx-users] performance issue with many short MD runs

Hi,I have to run a lot (many thousands) of very short MD reruns with gmx.Using gmx-2016.3 it works without problems, however, what i see is thatthe overall performance (in terms of REAL execution time as measured with the unix time command)which I get on a relatively new computer is poorer

Re: [gmx-users] Lipid water simulation

Hi, On 27-03-17 03:55, Sheikh Imamul Hossain wrote: > Hi all, > > I am trying to simulate 1024 dppc lipids with water. I have prepared my > system using Charmm-Gui monolayer builder. Then I converted the atomistic > system to coarse grained system using bacdward.py. The box size I got in > the

[gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

--- Begin Message --- Hello, I am a new user of gromacs. I am trying to calculate SASA for a protein system. I have used the command gmx sasa -f traj.trr -s md.tpr -o sasa.xvg -n index.ndx From this I can only get the total SASA but I want hydrophobic and hydrophilic SASA separately. I know

[gmx-users] Bond energy difference between CHARMM and GROMACS

I try to compare the energy in CHARMM and GROMACS. After running 4 systems I found the dihedral energies are the same, but the bond energies are different. Can somebody help me to solve this problem? (1)Only one residue: MET Bond: 0.44*4.18 = 1.839 (CHARMM) > 2.587 (GROMACS)