[gmx-users] AFM Simulation

Hi everyone. I'm doing a simulation of a system where a peptide is linked to a surface and an AFM tip is brought in contact to do force measurements. The AFM tip moves very slowly (1nm/ms), so I'm simulating stationary tips at various distances. Does anyone know the most direct measurement

[gmx-users] data points missing

Dear users, In one of the simulations I have run, I have transfered it from one system to another so some data points were missing what I should do now. how to find which data points are missing? Thank you With regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: data points missing

Dear users, gmxcheck on the .xtc file shows that simulation has run for 100ns but while calculating energy terms using ener.edr file, it gives nan error - Energy Average Err.Est. RMSD Tot-Drift

Re: [gmx-users] Re: data points missing

On 14/06/2011 6:09 PM, Kavyashree M wrote: Dear users, gmxcheck on the .xtc file shows that simulation has run for 100ns but while calculating energy terms using ener.edr file, it gives nan error - Sounds like you have managed to calculate only on a subset of your data. I'm guessing

[gmx-users] Re: Dissociation of Ligand-reg

Sir, The simulation system consists of enzyme, two substrate and one native ligand (protein, glutathione and NADPH + FAD) actually I am interested in manifesting substrate (GSH of GSSG and NADP+ of NADPH) dissociation from the protein after reduction reaction. I here below mentioned an article

Re: [gmx-users] Regarding H-bond autocorrelation

I am using the Gromacs 4.5.3is that feature is present in this version.. On Mon, Jun 13, 2011 at 21:39, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, The problem is that g_hbond subtracts a background level to compensate for the finite size of the system. I thought that feature

[gmx-users] g_sas index files/hydrogen bonds

Dear Gromacs Users, I am calculating the hydrophobic interface area using g_sas between ligands (their hydrophobic solvent accessible surface area (SASA) 95%) and hydrophobic residues of coiled coil fragment of protein (two helical strands) as follows: Protein SASA + ligand SASA -

Re: [gmx-users] MD - analysis

Kavyashree M wrote: Dear Sir, g_mindist analysis showed the violation of minimum image convention, it was violated over a short period of time and then it came back to normal. I attach the plot herewith. Should this data be discarded or any useful information can be obtained. You've

[gmx-users] Problem with 512 membrane

Dear Gro users, We created an all-atom system with 512 DPPCs by the method which was suggested by Justin (genconf -f 128.gro -o 512.gro -nbox 2 2 1) and a CG system with 512 DSPCs by using Martini self assembly tutorial. We do get nice bilayers, however after minimization, the systems break

Re: [gmx-users] Problem with 512 membrane

Du Jiangfeng (BIOCH) wrote: Dear Gro users, We created an all-atom system with 512 DPPCs by the method which was suggested by Justin (genconf -f 128.gro -o 512.gro -nbox 2 2 1) and a CG system with 512 DSPCs by using Martini self assembly tutorial. We do get nice bilayers, however after

[gmx-users] mdrun -nc

Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. It also amazing me when I type top to check the job, only one process in computer and the CPU utility

Re: [gmx-users] mdrun -nc

Hsin-Lin Chiang wrote: Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. I assume you mean -nt? It also amazing me when I type top to check the

[gmx-users] Questions about GB parameters

Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings myself. The discussion in question is here: http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html I wanted to post a

Re: [gmx-users] mdrun -nc

On most of my multi-core machines, an attempt is made to detect the number of threads to start at run-time (there may be a check for the MAXIMUM number of threads at compile-time, but a developer would need to chime in to determine if this is the case). For instance, I have a dual quadcore machine

Re: Re: [gmx-users] Water Potential Energy

Dear Mark, Thanks for the reply! I am using the same NPT conditions except time constants. The simulation was performed at constant temperature (300K) and pressure(1 bar) using velocity rescaling algorithm (tau=0.1 ps) for temperature coupling and Berendsen coupling scheme (tau=1 ps) for

Re: [gmx-users] Questions about GB parameters

Hi! Hmm.. Let me see if I can shed some more light on this. It's been a while though since I visited the literature here, and also my laptop broke down today, so I need to take of that first before I can check the code! Thanks /Per 14 jun 2011 kl. 20:24 skrev Justin A. Lemkul

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

Dear Justin, I have run into another problem. I created the system by including DHB in vwdradii.dat as follows: ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ;

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

shivangi nangia wrote: Dear Justin, I have run into another problem. I created the system by including DHB in vwdradii.dat as follows: ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*'

[gmx-users] Question about umbrella sampling through a nanotube

Dear GMXers, I'm trying to compute the PMF of a molecule along the centerline of a nanotube (the axial direction of the nanotube is parallel to the z axis). The nanotube is used as the reference group and the molecule as the pulling group. pull_geometry = position pull_dim= Y Y Y

[gmx-users] Question about umbrella sampling through a nanotube

Unfortunately, I don't think that there is any way to use this data (and only this data) to derive the PMF along z. The way that you did your US, the PMF along z is convoluted with xy motion. You can get the PMF along the reaction coordinate that you actually used (XYZ) using standard WHAM

Re: [gmx-users] simulating a protein homodimer

Stephen Edgcomb wrote: Hello All I am trying to simulate a protein homodimer. My command lines are: pdb2gmx -f dimer.pdb -p dimer.top -o dimer.gro -ignh -ter -chainsep interactive grompp -f minim.mdp -c dimer.gro -p dimer.top -o input.tpr mdrun -nice 0 -v -s input.tpr -o minim_traj.trr

[gmx-users] trjconv with superposition

Dear Colleagues, I want to extract PDB snapshot from trajectory file by following command. It works in 4.0, but not in 4.5 pdb=1akk trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc trjconv -s ${pdb}_gromos53a6_MD2.tpr -f ${pdb}_gromos53a6_MD2.traj.xtc -dt 20 -b 0 -o

Re: [gmx-users] trjconv with superposition

Liu Shiyong wrote: Dear Colleagues, I want to extract PDB snapshot from trajectory file by following command. It works in 4.0, but not in 4.5 pdb=1akk trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc trjconv -s ${pdb}_gromos53a6_MD2.tpr -f