[gmx-users] .itp file for cyclohexane (gromos96 FF)

Hi everybody, I was wondering if anybody has, and is willing to send me, a .itp file for cyclohexane with gromos96 parameters. I searched the list, but could not find any. I apologize if I've missed it in the list. Thank you very much, Isabella ___

[gmx-users] g_sas with 3.3 and 3.3.2 gives different results

../traj1_12_1micro_System_dt100ps.xtc -e 100 -s topol332.tpr -o area332.xvg 0 37.7036 50.8631 88.5667 0 Am I doing something stupid or is it a bug? Thanks, Isabella - Dr. Isabella Daidone Computational

Re: [gmx-users] Re: editconf -d

Hi, this is what is written in one of the options in editconf: " -[no]c bool no Center molecule in box (implied by -box and -d)". Moreover, in the mailing list you can find discussion about this topic with version 3.2 and David said it was a bug (that -d -c did not really center). So I w

[gmx-users] Re: editconf -d

I try again, just to know if it is not true that -d implies centering... Hi, when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at the corner of the box. In gromacs version 3.3, does option -d in editconf really imply that the protein will be c

[gmx-users] editconf -d

Hi, when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at the corner of the box. In gromacs version 3.3, does option -d in editconf really imply that the protein will be centered or is there still a bug (as in version 3.2.1) or am I missing some

Re: [gmx-users] rvdw

ella, The Gromos force fields were parameterized for use with a rvdw cutoff of 0.9. Other cutoffs may introduce artefacts. Ciao! Tsjerk On 6/21/06, Isabella Daidone <[EMAIL PROTECTED]> wrote: Sorry, but I'm a little bit confused about what rvdw to use for simulations of proteins in s

[gmx-users] rvdw

I see that with version 3.3 is now possible to use rvdw>rcoulomb. So I guess rvdw=1.4 should be used. What about simulations done with version 3.1.4, where rvdw=0.9 nm was used? How to justify that? Thanks Isabella ___ gmx-users mailing listgmx-u

[gmx-users] rvdw

Sorry, but I'm a little bit confused about what rvdw to use for simulations of proteins in solution with gromos96 force field while using pme for coulomb interactions. In the gromacs 3.3 manual I still read (with pme): rcoulomb=rlist=rvdw=0.9 nm Then, I found in the discussion list (+ the paper