Re: [gmx-users] difference between steep and cg

Hi Ming Tang, See https://en.m.wikipedia.org/wiki/Gradient_descent It has a further link to CG. Cheers, Tsjerk On Jul 11, 2015 4:10 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Gromacs experts, I am quite confused about the difference between the energy minimization algorithm steep and

[gmx-users] question

Dear Mark, Thanks for your attention, If I want to use PRODRG server and not ATB for my ligand, how to modify charge and charge group number? I am beginner in this acse, please guide about that. Best wishes, Atila -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] g_hbond

Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?

[gmx-users] RB dihedral type in amber99sb-ildn ffbonded.itp

Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the ligand.itp externally, I can not impose the distance restraints between the protein and the ligand.

Re: [gmx-users] Simulation with ligand on protein surface

Hi Justin and sorry for the vagueness What I'm observing are displacements from the binding site (granted, they are quite shallow) and loss of any relation to the experimental data. They also happen fairly fast (often below 10ns) and just looking at the trajectory, makes me think something is

Re: [gmx-users] g_hbond

Hello Erik, I did the same. Thanks, Nilesh Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I don't understand why am I

Re: [gmx-users] GPU gromacs

Thanks Slizard. I need to get this simulation done in a week but does not have the right facilities. Is there anyone in the group with some high end GPU cards that can help me get this running. Cheers James On Tuesday, July 7, 2015, Szilárd Páll pall.szil...@gmail.com wrote: Of course you can,

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)

On 7/10/15 7:15 PM, Nathan K Houtz wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)

On 7/10/15 7:21 PM, Justin Lemkul wrote: On 7/10/15 7:15 PM, Nathan K Houtz wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to

[gmx-users] on VMD analysis of the gromacs production MD

Dear All, After energy minimization, 100 ps NVT md and 100 ps NPT md (based on the on-line lysozyme tutorial), I have processed a 30 ns production MD (also based on the on-line lysozyme tutorial). Then I load the NPT.gro and the 30ns_production_md.xtc to the VMD, and by VMD I find in the

Re: [gmx-users] RB dihedral type in amber99sb-ildn ffbonded.itp

On 7/11/15 2:21 AM, tarak karmakar wrote: Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the ligand.itp externally, I can not impose the distance

Re: [gmx-users] question

On 7/11/15 3:43 AM, Atila Petrosian wrote: Dear Mark, Thanks for your attention, If I want to use PRODRG server and not ATB for my ligand, how to modify charge and charge group number? I am beginner in this acse, please guide about that. Shameless self-promotion for the millionth time:

Re: [gmx-users] Simulation with ligand on protein surface

On 7/11/15 2:51 AM, adam zalewski wrote: Hi Justin and sorry for the vagueness What I'm observing are displacements from the binding site (granted, they are quite shallow) and loss of any relation to the experimental data. They also happen fairly fast (often below 10ns) and just looking at

Re: [gmx-users] question

And now I have a reference for when I tell people that PRODRG is utterly useless. Thank you. JL On 7/11/15 3:43 AM, Atila Petrosian wrote: Dear Mark, Thanks for your attention, If I want to use PRODRG server and not ATB for my ligand, how to modify charge and charge group number? I

Re: [gmx-users] Adding missing heavy atoms

On 7/11/15 1:03 AM, prasun kumar wrote: Dear All I have generated the base atoms of nucleotides in a structure, but it does not have sugar and phosphate atoms. Is there any method by which I can add them appropriately (either in A or B form) If you already have the base configuration, you

[gmx-users] H-bonding autocorrelation function

Hi, I have a question about the H-bonding autocorrelation function, if I have a trajectory, say 1-1-1-1-1-1-0-1 (1 is H-bonding, 0 is no H-bonding), the time step is 0.006 ps, the correlation is equal to h(0)h(t) / h(0)*h(0), my answer is at t = 0.006, correlation = 7/7 = 1; at t = 0.012,

[gmx-users] Reaching the desired pressure and density

Hi, Dear users,I have created a box of polymer with about 50 molecules. I'm performing NPT runs to reach to the pressure of 1 bar. After a long time of simulation (15 ns) the average pressure is still about -0.5 and the density has saturated to around 700 kg/m^3 which should become 1200 kg/m^3