Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

. Kushal Seth On 6/9/06, Arneh Babakhani <[EMAIL PROTECTED]> wrote: No ions, it's a neutral system. The order of DMPC and Water, in what sense? In the gro file, the proteins come first, then the DMPC residues, then the water. The order is similar in the [system] part of my top fi

[gmx-users] Order parameter

Hi All ! Can anyone help me to find the order parameter of cholesterol as a function of distance form the bilayer. I am doing a Lipid bilayer simulation with POPC and Cholesterol. Thanks a lot in advance. Kushal Seth ___ gmx-users mailing listgmx

[gmx-users] Probabilty distribution

Hi all ! I was trying to compute the probability distribution for an angle in the lipid chain. I would like to know how can i do it. Thanks in adance. Kushal Seth ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] Problems with pdb2gmx and grompp

Hi I had the same problem. Check your MDP file or may be try using another mdp file (which you might get on gromacs queries ) inserting the parameters you want. Also for your other error try including the files ffgmx.atp , ffgmxnb.itp , ffgmsbon.itp and ffgmx.itp in the directory you are working

[gmx-users] EM comparison

e time my Fmax also converges to < 100. WHY SO? Please comment ! Thanks in ADVANCE. Kushal Seth ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the

Re: [gmx-users] MD run error

otropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 0.5 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529  Thanks in advance Kushal       On 4/11/06, Mark Abraham <[EMAIL PROTECTED]> wr

[gmx-users] MD run error

Hi all ! I am running a MD simulation and i got "Warning: 1-4 interaction between 1 and 6 at distance 1.102 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in

Re: [gmx-users] Membrane error

Dear All! Thanks for your replies.My CPP path seems to be ok as far as the location is concerened and I continue to get the same error messsages. Is there any other reason for that ( my top files also seem to be wroking for other simulations ) Need help ASAP. Thanks again to you all. Kris   On 4/4/

[gmx-users] Membrane error

HI all !I am gettting this error  while doing my simulation... for the bilayersBack Off! I just backed up emout-nowater.mdp to ./#emout-nowater.mdp.1#checking input for internal consistency..ling /usr/bin/cpp: No such file or directorycpp exit code: 32512-I/usr/local/gromacs/share/gromacs/to

Re: [gmx-users] cluster

hi all ! I am trying to run the following command - grompp -np 2  -v -f em.mdp -po emout-nowater -cbinaryCR-Ochol-box-largeZ.pdb -p mytop-nowater1.top -o em-nowater.tprbut i am encountering this problem,checking input for internal consistency... ...ling /usr/bin/cpp: No such file or directorycpp ex