Re: [gmx-users] Fwd: sds topology // prodrg vs. am1-bcc // charges

Louic Vermeer wrote: Hi gromacs users, I want to use a topology file for SDS and obviously I am not the first person doing simulations in SDS. Previous comments on this list suggested using the prodrg server, but I also read that the partial charges calculated by prodrg are not always reliabl

[gmx-users] How does g_msd calculate the deviation of diffusion coefficient?

Hi, Every time I use g_msd to calculate the MSD for one group, this program always output the diffusion constant like # D[ SOL] = 0.4996 (+/- 0.0366) (1e-5 cm^2/s) I know that g_msd calculates the D using the least square (LSQ) method. But I dont know how to calculate the deviation of D

[gmx-users] Question about trjorder

Dear GMX-users, I'm using Gromacs 3.3.1, and trying to collect solvents within specific distance from a part of peptide. I typed "trjorder -f *.xtc -n *.ndx -s *.tpr -o -nshell -da 8 -na 12 -r 2.5". I correctly typed reference molecule, and the result of -nshell looks OK, but couldn't get the

Re: [gmx-users] problem with pdb2gmx and ffG43a1p

the phosphorilated Ser is not defined in the G43a1 force field. You must define it. See manual for instructiion. XAvier I am trying to perform simulation of a phosphorylated protein (phos. on a Ser residue). I am tring to use *ffG43a1p as my forcefield. When I add a phosphate to the Ser, mod

[gmx-users] problem with pdb2gmx and ffG43a1p

Hi All, I am trying to perform simulation of a phosphorylated protein (phos. on a Ser residue). I am tring to use *ffG43a1p as my forcefield. When I add a phosphate to the Ser, modify SER to SEP and run pdb2gmx it gives me this : *** WARNING: atom HG1 is missing in residue THR 1 in the pdb file

RE: [gmx-users] Hessian Matrix Doubt

From: Anirban Ghosh <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GROMACS Subject: [gmx-users] Hessian Matrix Doubt Date: Fri, 3 Aug 2007 06:55:34 +0100 (BST) Hi All, I want to go for Normal Mode Analysis of a protein in water. I have done the energy minimization of t

[gmx-users] Fwd: sds topology // prodrg vs. am1-bcc // charges

Hi gromacs users, I want to use a topology file for SDS and obviously I am not the first person doing simulations in SDS. Previous comments on this list suggested using the prodrg server, but I also read that the partial charges calculated by prodrg are not always reliable. What would be the m