[gmx-users] Checksum wrong

Dear users, When I restart one of lambda points for free energy calculation, Gromacs gives the following error. Whereas the md_0.xvg file exists in the folder. I hope the md_0.xvg can append? Command: mdrun -v -s md_0.tpr -cpi md_0.cpt -cpo md_0-1.cpt -dhdl md_0.xvg -x md_0.xtc -e md_0.edr -g

Re: [gmx-users] Making disulfide bonds between protein and glutathion (GSH)

Many thanks Justin :) Tuong Vy 2015-05-28 21:01 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/27/15 10:23 PM, Vy Phan wrote: Dear Gromas User, I want to making disulfide bonds between protein and glutathion (GSH). The topology for GSH I got from Produg serve. Don't do this; the

[gmx-users] Cyclohexane simulation problem

Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box  using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3 volume)after run several times and convergence

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

Hi Not because I developed ACPYPE, but if I’d like to be the most rigorous as possible, I’d go with ACPYPE and RED (http://q4md-forcefieldtools.org/). Alan On 29 May 2015 at 20:53, Ebert Maximilian m.eb...@umontreal.ca wrote: I continued to define good partial charges using the tools

[gmx-users] regarding pdb2gmx

Hi all, I have a general query about the basic functioning of pdb2gmx. I recently observed that when I take a PDB file for a DNA molecule and build its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it without any hitches. If I look at the .itp file made for the DNA chain it

Re: [gmx-users] regarding pdb2gmx

On 5/30/15 6:40 AM, soumadwip ghosh wrote: Hi all, I have a general query about the basic functioning of pdb2gmx. I recently observed that when I take a PDB file for a DNA molecule and build its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it without any hitches. If I

Re: [gmx-users] Cyclohexane simulation problem

On 5/30/15 3:44 AM, mohsen shahlaei wrote: Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3

Re: [gmx-users] Should I fix my drugs during membrane penetration simulation?

On 5/30/15 1:25 AM, yoochan wrote: Dear all, I’m trying to do umbrella sampling simulation which drugs penetrate the POPC membrane. I have trouble what if I do npt or umbrella simulation, the drugs move around from the initial location. (I got each 0.1 nm spacing window for npt and

Re: [gmx-users] Cyclohexane simulation problem

Please keep the discussion on the mailing list. On 5/30/15 8:44 AM, mohsen shahlaei wrote: Dear Justin, Thanks, could you please explain what is difference between Cut-off and PME in calculation of electrostatic interactions Simply, a cutoff is what it says it is - a plain truncation at a

Re: [gmx-users] regarding pdb2gmx

Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my previous works actually the DNA molecule gave

Re: [gmx-users] regarding pdb2gmx

On 5/30/15 10:24 AM, soumadwip ghosh wrote: Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my