Re: [gmx-users] Gromacs 4.6 Installation under Cygwin

On Sat, Feb 23, 2013 at 3:41 AM, Mirco Wahab < mirco.wa...@chemie.tu-freiberg.de> wrote: > On 23.02.2013 01:59, toma0...@umn.edu wrote: > >> Hello, >> I am trying to install Gromacs 4.6 on a Windows workstation under >> cygwin. After I install everything, when executing g_luck I come up with

[gmx-users] Re: GB parameter(s) missing or negative but they aint missing nor negative

Hi everybody and thanks to you all, i have the same problem solved modifying the gsba.itp in the right path, but where did u take the values for the others O5, N*, CK and P? Regards, D. -- View this message in context: http://gromacs.5086.n6.nabble.com/GB-parameter-s-missing-or-negative-but

Re: [gmx-users] coordination number per residue

On 2/24/13 12:53 PM, benrezkallah djamila wrote: Hello everybody, I am working on a system consisting of protein-ions in water box. I need to calculate the coordination number per residue for my protein, I have searched the gmx mailing list, and, I have not find the solution. please, can you

[gmx-users] Spectrum reproduction

Dear gromacs users, I have been studying the association between a protein and an electrode by MD simulation. In particular I am interested in the relative orientation in respect to the surface. I only have the PM-IRRAS spectrum of the complex. I am wondering if someone knows a method or a softwar

Re: AW: [gmx-users] g_current

Hello, My system is ionic liquids composed of 128 cation (EMIM) and 128 anion (ethyl sulfate). I choose system (0) as index group. Nilesh > Hi, > > Can you be a little bit more specific about your system, and what you > have > chosen as index groups ? > > /Flo > > --- > Florian Dommert > D

[gmx-users] Coupling only a variable solvent subgroup to the thermostat

Dear GROMACS users, In a NPT molecular dynamics simulation of a system composed by a water box with ions and a protein I want to couple only water molecules which are far from the protein to the Nosé-Hoover thermostat and leave the remaining system uncoupled. I managed to couple a subse

[gmx-users] Error during npt equilibration in coarse grained simulation

Dear users, I am trying to do a coarse grained simulation of an octamer of a 350 residue protein in water using gromacs-4.5.3 using martini force field. I got the following error when i started running NPT equilibration "Step 32, time 0.64 (ps) LINCS WARNING relative constraint deviation after LI

[gmx-users] Simulation problem

Hi. I've been running some polymer simulations on our cluster and I'm getting this error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. What does this error mean? I imagine it is somehow related to the