[gmx-users] Too many LINCS warnings with CaDA model, User-defined potential, Stochastic dynamics integrator

Dear All, Using GROMACS-5.1.4, I am trying to reproduce the results of a metal-ligand coordination-directed self-assembly study. The metal ion Pd(II) is represented using a CaDA model where four identical dummy atoms each with charge +0.5 are coplanarly attached to the Pd with charge

[gmx-users] (no subject)

Hello Everyone, I want to calculate some properties of the solvent molecules within 6angstrom from the protein backbone, for that I need a index group which only contain that number of solvent molecules in the index.ndx file so that I can specifically select that index to calculate different

[gmx-users] (no subject)

Hello Everyone, I want to calculate some properties of the solvent molecules within 6angstrom from the protein backbone, for that I need a index group which only contain that number of solvent molecules in the index.ndx file so that I can specifically select that index to calculate different

[gmx-users] pdb2gmx error due to terminal capping of peptide

Hi GMX users, 1. I drew the structure of my target peptide on Pymol, added amide capping group (NHH) at C terminus of peptide 2. Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh 3. Chose AMBER99sb-ildn force field which has parameters for NH2 capping group 4.

Re: [gmx-users] Density of a droplet in spherical coordinate

You MIGHT be able to use the vmd plugin membplugin to measure the density https://sourceforge.net/p/membplugin/wiki/Home/ treating the sphere as a membrane or if you know the total density and the radius you should be able to construct an

Re: [gmx-users] Density of a droplet in spherical coordinate

gmx spatial, then covert the g(xy,z) from the output file into the d(r, *ϴ,ϕ) you require?* Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

[gmx-users] Density of a droplet in spherical coordinate

Dear gmx user, I have a droplet of some short molecules (it is not perfectly spherical though), I was wondering how to calculate the density of each molecule type respect to center of the droplet. In other words the question is how the density of each molecule type varies in the spherical

Re: [gmx-users] Bennet error in FEP-calculations for charged ligands.

Michael, Thank you so much for such a quick and detailed response. I tried to increase the number of intermediate lambda windows, but unfortunately, it was not possible to reduce the error to an acceptable level. coul-lambdas = 0.0 0.02 0.05 0.08 0.12 0.16 0.2 0.3 0.4 0.6 0.7 0.8 0.84 0.88 0.92

Re: [gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.

Hi Mark, Thanks. Though I understood about gen-seed which is irrelevant once the velocity has been generated (from Boltzmann distribution) but still I am a bit confused about ld-seed. Is this ld-seed has a dependence to the configuration of the machine i.e. no of cores and processor...?

Re: [gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.

Hi, On Thu, 24 Jan 2019 at 10:22 Maity, Sayan wrote: > Hi Mark, > > > So basically, in order to reproduce the simulation, I need to fix both > seed numbers in the .mdp file right ...?? > No, I said the seeds were fixed *after* you run grompp. That is, the .tpr is in principle reproducible,

Re: [gmx-users] Nonsense timing accounting with OpenCL in Haswell

Hi Elton, It is very unlikely that you would be able to get any speedup with OpenCL with that CPU. For its generation the CPU is powerful but the GPU is a lower tier. To get meaningful speedup compared to running on i7 CPU you want to have a GT3 or higher GPU with at least 48EUs. Yours has

Re: [gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.

Hi Mark, So basically, in order to reproduce the simulation, I need to fix both seed numbers in the .mdp file right ...?? However, I can find the ld-seed number from the .log file but I didn't find any gen-seed number. So in which file I could get the gen-seed number if the previous

Re: [gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.

Hi, Both these seeds are fixed after you run grompp. That has no relationship to whether velocities are present from any input file. There is also no difference between NVT and NPT. I assume that your non-reproducible cases are each running grompp with one of these seed values set to -1, in