[gmx-users] Re: gmx-users Digest, Vol 86, Issue 84

Dear Sir/Madam, Please help me to find that why we need to run NVT and then NPT in equilibriation run and not the vice-versa. Thank you in advance Ravi Kumar V IPC dept., IISC, INDIA. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

Re: [gmx-users] Re: gmx-users Digest, Vol 86, Issue 84

On 14/06/2011 5:10 PM, Ravi Kumar Venkatraman wrote: Dear Sir/Madam, Please help me to find that why we need to run NVT and then NPT in equilibriation run and not the vice-versa. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation Mark -

Re: [gmx-users] data points missing

On 14/06/2011 4:24 PM, Kavyashree M wrote: 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? I don't agree with your guess that transferring to n

[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 t

[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 ref

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 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 had been taken

[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 - Protein&Liga

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 go

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

ITHAYARAJA wrote: 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

Re: [gmx-users] g_sas index files/hydrogen bonds

On 14/06/11, "Marzinek, Jan" wrote: > > > > > > > > > > > > > > > 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 coi

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

Could be. But, if memory serves me right, there's another dataset in the output, which shows the acf without the "background subtraction". Erik 14 jun 2011 kl. 12.10 skrev bipin singh: > I am using the Gromacs 4.5.3is that feature is present in > this version.. > > On Mon, Jun 13,

[gmx-users] rdf

Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to study is there any bifurcated interaction between hydrogen of cation and CL atoms or CL atom interacting with 2 different hydrogen of cation. For this I considered all CL atoms are distinguishable. I am thinking to run

Re: [gmx-users] rdf

On 14/06/2011 10:11 PM, Nilesh Dhumal wrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to study is there any bifurcated interaction between hydrogen of cation and CL atoms or CL atom interacting with 2 different hydrogen of cation. For this I considered all CL a

[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 apar

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 minimiz

[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 utilit

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 j

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

Thanks Justin, vdwradii.dat suggestion worked :) On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello dear gmx-users, >> >> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as >> the solvent ( with a positively charged protein a

[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 couple

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 pre

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" : > > Hi All

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 ; 'AAA

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 '*' matc

[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 pull_s

[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

[gmx-users] simulating a protein homodimer

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 -c minimized.gro -e minim_ener

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 ${pdb}_gromos53a6_MD2.

[gmx-users] g_density

Hi, I have aligned a trajectory to a reference structure and have now run g_density on both the original and the aligned trajectory in order to find the bilayer headgroup position and the bilayer thickness. g_density works fine with the original trajectory but there seems to be a bug when running

[gmx-users] Re: 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. / I assume you mean -nt? Sorry, -nc is a typo of -nt. >/ It also amazing me w