[gmx-users] Free energy calculations with pull code and umbrella sampling

Hi All, I have one quick questions about free energy calculations via pull code+umbrella sampling. (see below for some further information on what I am trying) First of all I think Justin is right umbrella sampling is much more straightforward. In particular in my situation where I see

Re: [gmx-users] g_rms with two trajectories

After some further search I found this very useful script which converts xpm to digits. This has solved my problem. #!/usr/bin/env python import sys def unquote(s): return s[1+s.find(''):s.rfind('')] def uncomment(s): return s[2+s.find('/*'):s.rfind('*/')] def col(c): color =

[gmx-users] Insufficient disk space error

Dear Gmx User, I was running a simulation in Ubuntu 14.0 for 20 ns. I have a total disk space of 120 GB. I was running the sim from Downloads/Gromacs/build folder. But after runing 9 ns, the siom stops giving an error message insufficient disk space. I have check the space it have more than 110

Re: [gmx-users] Umbrella Sampling and histograms smoothness

On 2/9/15 8:55 PM, Agnivo Gosai wrote: Dear Users Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating the topology and the itp files. Therein , automatic position restraints are generated. Now, I have never used manual restrain force constants. If you're using the

Re: [gmx-users] Umbrella Sampling and histograms smoothness

Dear Users Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating the topology and the itp files. Therein , automatic position restraints are generated. Now, I have never used manual restrain force constants. Could any user suggest any source / literature for choosing

Re: [gmx-users] A question regarding electrostatic and coulomb energies.

On Mon, Feb 9, 2015 at 12:40 PM, IÑIGO SAENZ inigo.saen...@estudiant.upf.edu wrote: Dear Mark, I've been researching about energy groups and I think that it isn't the solution for my problems. The background of my question is the following: I'm currently working with the people that

Re: [gmx-users] Cluster recommendations

Note that perf/W or perf/buck of a certain simulation on a certain hardware can be quite misleading. Currently we balance CPU-GPU load by shifting long-range electrostatics work to the short-range kernels. This involves a tradeoff which does not always give the benefit one may expect and that's

Re: [gmx-users] Umbrella Sampling and histograms smoothness

On 2/9/15 4:11 PM, Agnivo Gosai wrote: Dear Users My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's tutorial advocates a 10 ns simulation time. I found that after running WHAM , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my histograms have two

Re: [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

On 2/9/15 11:00 AM, Agnivo Gosai wrote: Hi Antara Did you check the plot of the potential energy against the simulation time ? You can visualize the convergence of your energy minimisation from the above plot. Energy minimization, by definition, converges to some value (but there is no

[gmx-users] Umbrella Sampling and histograms smoothness

Dear Users My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's tutorial advocates a 10 ns simulation time. I found that after running WHAM , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my histograms have two peaks!! So should I increase the simulation

[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints

Hi, I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied position restraints as well as had vdwradii.dat file for genbox step. Yet after minimisation, there are gaps between the lipid molecules. Pls suggest a remedy. -- Regards, Antara -- J.R.F.(Project) Systems Biology

[gmx-users] A question regarding electrostatic and coulomb energies.

Dear Mark, I've been researching about energy groups and I think that it isn't the solution for my problems. The background of my question is the following: I'm currently working with the people that develops ACEMD and because of that I've got access to some information that ACEMD uses for its

Re: [gmx-users] g_rms with two trajectories

Dear Erik, I have the matrix and I converted it with xpm2ps into a coloured image. I want to compare the ligands at the same time so I would be interested in the diagonal. Which is the best way to get from the xpm matrix the diagonal plotted in 2d as a function of time and rmsd value? Best

[gmx-users] g_rms with two trajectories

Dear Gromacs Users, I want to calculate the rmsd between two ligands - the system is exactly the same, just the ligand binding conformations are different. Therefore i want to use g_rms with the option -f2 as in the following command: g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o In g_rms

Re: [gmx-users] Umbrella Samling Alteration

On 2/8/15 5:53 PM, Alexander Law wrote: This method doesn't work. Does each simulation have to complete the 10 ns in order to move on the analysis step, or can I use incomplete simulations? Analyze however much time you like. If not, is there another possibility to force the simulations

Re: [gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS

On 2/9/15 7:34 AM, Antara mazumdar wrote: ​eRROR OBTAINED DURING NVT: ​ Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. ​NVT CONDITIONS WERE : ​ n for B2AR-POPC system define = -DPOSRES ; Protein is

[gmx-users] pH during free energy calculation

Dear Experts and users, I am running simulation for solvation free energy calculation using thermodynamic integration approach (as mentioned in Justin's tutorial). My system consist of a cation molecule, an anion molecule and bulk of solvent molecules. I want to understand the pH of my system,

Re: [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

On 2/9/15 7:41 AM, Antara mazumdar wrote: i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force

[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS

​eRROR OBTAINED DURING NVT: ​ Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. ​NVT CONDITIONS WERE : ​ n for B2AR-POPC system define = -DPOSRES ; Protein is position restrained (uses the posres.itp file

[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with

Re: [gmx-users] H-Bonding residues against specific frames

On 2/8/15 6:08 PM, Agnivo Gosai wrote: Dear Users I am using g_hbond to get the H-bonds for a particular simulation over the entire trajectory. In the log file I can find which reesidues are forming H-bonds. However , I want the H-bonds formed over the entire simulation length frame wise or

Re: [gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints

On 2/9/15 5:07 AM, Antara mazumdar wrote: Hi, I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied position restraints as well as had vdwradii.dat file for genbox step. Yet after minimisation, there are gaps between the lipid molecules. Pls suggest a remedy.

Re: [gmx-users] g_rms with two trajectories

Dear Julian, Use the -m flag. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 9 Feb 2015, at 12:20, Julian

Re: [gmx-users] pH during free energy calculation

On 2/9/15 7:42 AM, vivek sharma wrote: Dear Experts and users, I am running simulation for solvation free energy calculation using thermodynamic integration approach (as mentioned in Justin's tutorial). My system consist of a cation molecule, an anion molecule and bulk of solvent molecules. I

Re: [gmx-users] g_rms with two trajectories

Dear Julian, I see no other means than writing a script to parse out the diagonal. The xpm format is quite human readable so I don’t think it will take you long to figure out how to do. Kind regards, Erik On 9 Feb 2015, at 14:16, Julian julim...@gmail.commailto:julim...@gmail.com wrote:

Re: [gmx-users] g_rms with two trajectories

Juilan, A quick way to do this is with an awk script, such as: awk '{print $NR}' (your matrix.dat file here). This will print the diagonal of the matrix. If you want the one from the .xpm file you need to use something like: awk '{if($0!~/*/){print substr($0,counter+2,1),counter++}}' Though