[gmx-users] oplsaa force field

Sir, I studying the dynamics of membrane proteins.First I did a 20 ns simulation using GROMOS96 53a6.This force field cause some problems in the helical part of the protein.Now I am trying to do the same simulation with opls-aa force field.Is the changes I should have to do in ffnonbonded.itp

[gmx-users] (no subject)

sir, I am studying dynamics of a membrane protein using oplsaa force field. Energy minimization during nvt equilibration getting error like this. Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group

[gmx-users] segmentation fault

Sir, I am doing membrane protein dynamics in lipid bilayer, using oplsaa force field. When I am doing minimization after genion I getting message like this Back Off! I just backed up ions_1.tpr.trr to ./#ions_1.tpr.trr.2# ack Off! I just backed up ions_1.tpr.edr to ./#ions_1.tpr.edr.

[gmx-users] amber forcefield

sir, I am studying the dynamics of membrane protein.I want to use amber force field.Then what changes should I make in the ffnonbonded.itp and ffbonded.itp?Is it similar as in Justin manual?Is it necessary to convert C6 and C12 values in lipid.itp(for gromos) to values in terms of sigma and epsi

[gmx-users] problem with REMD

Respected Sir, Now I am trying an REMD simulation on a peptide in cluster. The command line I used as follows mpirun -np 6 /usr/local/gromacs/bin/mdrun_mpi -s sd_.tpr -multi 2 -replex 1000 -reseed 175320 But this command line getting error like this Wrote pdb files

[gmx-users] doubt in remd

Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

[gmx-users] doubt in mdrun

Sir, I studying the dynamics of a peptide in explicit solvent model.But during the mdrun I got the message like this. NOTE 1 [file md.mdp]: This run will generate roughly 1177130 Mb of data why the run generating this much amount of data? The md.mdp file I used is shown below title

[gmx-users] doubt in minimization part

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now I am confusing with the following ( shown at botom) part of the tutorial.Here minimization means to minimize system_inflated.gro, is it right? Then without .epr and .top files of system_inflated.gro how can I do thi

[gmx-users] error in grompp

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But grompp (before minimization of system_inflated.gro) giving error like this.. Fatal error: Atomtype LC3 not found Actually what changes I should do on the system topology, before grompp? I found that atomtype LC3

[gmx-users] generation of .itp file

sir, I want to generate .itp from a pdb file. Is there any option in gromacs. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please do

[gmx-users] error during minimization

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization getting error like this.. There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 18.5346 nm Change the number of nodes or mdrun opti

[gmx-users] removal of water

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC.I solvated the system using genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro . But system_shrink1_solv.gro contain some unwanted water molecules in between lipid. How to eliminate these water m

[gmx-users] error during minimization

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this error?plz give me a solution to overcome it. -

[gmx-users] convergence problem

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Output of energy minimization step is like this. Reached the maximum number of steps before reaching Fmax < 100 writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 100 in 20001 steps.

[gmx-users] error during nvt equilibration

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration and created index.ndx by using make_ndx. During this step I selected "16/14" and "1/13".The next step (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr) getting error like thi

[gmx-users] error during mdrun

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of thei

[gmx-users] segmentation fault

Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 485 and 490 at distance 3.8

[gmx-users] conformational change

Sir, I am studying the dynamics of a beta barrel shaped membrane protein. The starting end of the barrel is a helix which is inside the barrel. During salvation with genbox some water molecules entered inside the barrel.Then I did the 20 ns dynamics.After dynamics more number of water mole

[gmx-users] change in conformation

Sir, I am studying the dynamics of a beta barrel shaped membrane protein. The starting end of the barrel is a helix which is inside the barrel. During salvation with genbox some water molecules entered inside the barrel.Then I did the 20 ns dynamics.After dynamics more number of water mole

[gmx-users] remd analysis

Sir, I did an remd simulation in implicit solvent for a peptide.I want to compare the NOE distances from NMR and various conformations from REMD output. Here how I get various conformations from remd trajectory? .Is any script is available to find distance between two particular atoms?.How

[gmx-users] REMD

Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- gmx-users

[gmx-users] remd

Sir, I did a 10 ns REMD simulation for a peptide, 8 replicas using amber force field.Then extracted pdb file from the trajectory and clustered using g_cluster. The I viewed the average structure of the cluster in pymol .But here the atoms are merged togather.why it happends?Is there any pro

[gmx-users] remd

Sir, I trying to calculate ground state conformational ensemble of a peptide by comparing experimental chemical shift and predicted chemical shifts.For that I did REMD simulation at 8 temperatures.Then using g_cluster clustered.Here is it reasonable to compare the chemical shift of average st

[gmx-users] remd

Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how I can correlate experimental and theore

[gmx-users] remd

Hi Sir, Is it possible to run an REMD simulation having 16 replicas in a cluster(group of cpu) having 8 nodes. Here each node have 8 processors. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://w

[gmx-users] extraction of PDB from clusters.pdb

Sir, Using g_cluster I clustered snapshots in md trajectory using the command as follows g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl cluster

[gmx-users] remd

Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] (no subject)

sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Sear

[gmx-users] remd

sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Sear