[gmx-users] error in grompp

Hi everybody, I want do to an energy minimization and simulation with position restraints. Additionally to the protein I have a membrane around my protein which I also ant to fix. If I won't fix it, it is in the whole box after the minimization and simulation but not around my protein. Since I only

Re: [gmx-users] Re: specifying the direction of Pull in US

On 7/7/12 12:15 AM, Raj wrote: Thanks for ur suggestion Justin, I'm facing trouble in setting that vector, actually I cant figure out how can i set up a vector. Is there any easier way with which i can set up a vector. Thanks It can be set simply to the difference in the (x,y,z) coordinates

Re: [gmx-users] error in grompp

On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want do to an energy minimization and simulation with position restraints. Additionally to the protein I have a membrane around my protein which I also ant to fix. If I won't fix it, it is in the whole box af

Re: [gmx-users] Crashes during protein-ligand simulation

justin, It seems that problem was in the big charge groups in the ligand.itp file. In particularly I've devided largest group into several smaller and there haven't any crashes been occured yet. With my last system with the the default COM group I've obtained crash on the 25ns with the error abou

Re: [gmx-users] Crashes during protein-ligand simulation

On 7/7/12 11:08 AM, James Starlight wrote: justin, It seems that problem was in the big charge groups in the ligand.itp file. In particularly I've devided largest group into several smaller and there haven't any crashes been occured yet. With my last system with the the default COM group I've

Re: [gmx-users] BAR gives different result than TI

The implementation of BAR in gromacs is pretty hard for me to follow because of how everything is stored noncompactly in the histogram. In 4.6, both can be computed from the same dhdl.xvg file, so it might be easier to track down possible bugs. On Fri, Jun 29, 2012 at 2:24 PM, David van der Spoel

[gmx-users] Charmm foce field and free energy

Dear all, I'm trying to reproduce the hydration free energy of the methanol using the CHARMM force field. However I am getting a value considerably lower than the experimental: 17 kJ mol-1 (the experimental value is 21 kJ mol-1). Am I forgetting some technicality related to the force field? I usin

[gmx-users] bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

A gel-state all-trans lipid bilayer is going to be thicker than a liquid-phase lipid bilayer. I presume that you are starting far away from the all-trans conformation and I can imagine that this could lead to a net force that pushes the lipids apart. Inertia might just take it from there. You

[gmx-users] Dihedral potential - regd

Hello all, I am modifying parameters in gromacs by downloading charmm27.ff to my working directory, I have dihedral potential in my forcefield as v(T) = sumn over n = 0 to 6 an* (-1)**n cos **n (T) , with values from a0 to a6 , I haven't observed any dihedral potential related