[gmx-users] Re:comparison of energy between GROMACS and NAMD

Hi, I have performed minimization of ubiquitin in vaccum both in GROMACS and NAMD using CHARMM force field .when i have compared the energy values for first step ,i found that variation in the values NAMD (kcal/mol) GROMACS(kcal/mol) Bond 1929.36

[gmx-users] regarding top file

hello sir, i dono what i did was correct or not. But i did it. please tell me what i did was correct or not,, i tried two different ways to generate my top file. first i did prodrg for my whole lipopeptide and got its itp . pdb and gro file. then i included information about atomtype, bond, pairs

RE: [gmx-users] Test mail

ok Date: Sat, 17 Dec 2011 16:33:25 +0530 From: priya.thiyagaraja...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Test mail Greetings, THis is a mail to test my gromacs mailing list connection -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listi

[gmx-users] Gromacs is aborting without error during nvt equilibration

I have been trying to run simulations in Gromacs and have recently changed to the Gromos force field with SPC water from Charmm27. I am using the following equilibration script. title = NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator

[gmx-users] g_angle calculation

Hi all, I try to reproduce the results from g_angle using my own c++ code. Using the formula θ=acos(r_ij * r_kj/|r_ij||r_kj|) with the acos from the cmath library, I obtain an angle which is always ~5% larger when the angel calculated by g_angle. Does g_angle use the same formula or does it calc

Re: [gmx-users] About Choice PDB

vidhya sankar wrote: Dear justin,, Thank you for your immediate reply. Which PDB is suitable Either X-ray PDB (brookavean protein data bank) or NMR PDB to study the effect of ionic strength on protein. If i use x-ray PDB will it affect the result though i solvate and neu

Re: [gmx-users] energy_terms

balaji nagarajan wrote: Dear Users I have a peptide, (1AKI.pdb) My aim is to solvate it in the presence of the explicit water molecules and do minimization and to split the energy terms , and to see the energy contribution from each terms for this i have done the following in gromacs

[gmx-users] energy_terms

Dear Users I have a peptide, (1AKI.pdb) My aim is to solvate it in the presence of the explicit water molecules and do minimization and to split the energy terms , and to see the energy contribution from each terms for this i have done the following in gromacs -

[gmx-users] About Choice PDB

Dear justin,,     Thank you for your immediate reply. Which PDB is suitable Either X-ray PDB  (brookavean protein data bank) or NMR PDB  to study the effect of ionic strength on protein. If i use x-ray PDB will it affect the result though i solvate and neutralise the PDB before e

Re: [gmx-users] discrepancy between ED motions and the MD motion

Thanks Tsjerk Can you plz tell me How do we really conclude that an biologically relevant motion or a simple relaxation ( i have followed this approach, i also carried out a elastic netwok modelling based PCA and comapred the lowest mode obtained from EN-NMA with my PC1- Is this a right approach?

Re: [gmx-users] EM curve question

parto haghighi wrote: Dear Mark, Thanks for your answer. I have done these steps: 1. Prepare ligand topology by PRODRG server (like fifth gromacs tutorial) Did you adequately correct the parameters therein? As noted in that tutorial (and elsewhere), the charges and charge groups produced by

Re: [gmx-users] about umbrella sampling

vidhya sankar wrote: Dear Justin, Thank you for your immediate reply amidst of your busy schedule I am trying to pull one of chain of my protein using umbrella option of gromacs (As did in your website tutorial) After umbrella pulling i have extracted all frame of .

Re: [gmx-users] discrepancy between ED motions and the MD motion

Hi Vijayan R., Eigenvectors are specific up to a sign. So it's not said the start will end up as the negative extreme. It seems your interpolation just shows what happens in reverse. As a sidenote, do check whether it is a biologically relevant motion, or merely relaxation. Cheers, Tsjerk On De

[gmx-users] EM curve question

Dear Mark, Thanks for your answer. I have done these steps: 1. Prepare ligand topology by PRODRG server (like fifth gromacs tutorial) 2. Download lipid.itp file and make new force field for it (like second gromacs tutorial) 3. Use editconf and cat to prepare a system with 12 ligand in both sides of

[gmx-users] about umbrella sampling

Dear Justin, Thank you for your immediate reply amidst of your busy schedule I  am trying to pull one of  chain of my protein   using umbrella option of gromacs (As did in your website tutorial)  After umbrella  pulling i have extracted all frame of .gro  from .trr files .

[gmx-users] discrepancy between ED motions and the MD motion

Hi all I carried out a distance analysis between two domains with respect to time based on the center of mass. Subsequently i also carried out a PCA based essential dynamics to identify the global/biologically relevant motions. The strange and inconsistent result i find here is when i calculate

Re: [gmx-users] Protein Chains Spatially Separated After Energy Minimization

Benjamin Er wrote: Hello Everybody, I have 2 different protein chains (not a homodimer), chain C and chain F in a PDB file. These 2 proteins are interacting proteins close in proximity. I would like to use energy minimization (EM) and equilibration (EQ) to approximate the most relaxed inter

[gmx-users] Protein Chains Spatially Separated After Energy Minimization

Hello Everybody, I have 2 different protein chains (not a homodimer), chain C and chain F in a PDB file. These 2 proteins are interacting proteins close in proximity. I would like to use energy minimization (EM) and equilibration (EQ) to approximate the most relaxed interacting conformation betwee

Re: [gmx-users] Re: LINCS error

I did few changes ie decreased the time step/ increased the equilibration steps/ omitted the generation of velocity in production run / did 2 steps of equilibration / checked the starting structure for steric clashes. I don't understand what else should I try to fix the lincs warnings. Sent f