[gmx-users] qm mm and charges in GMX!

Hi GMX'ers, i've been reading some publications about QM MM calculatiosn intending to aplly this in my system. Since I'd read the GMX Manual and I have some doubts about this recent implemetationat the program. I'd compile the gromacs with MOPAC 2007 and when I tried to simulate at hybrid lev

Re: [gmx-users] qm mm and charges in GMX!

Hi GMX'ers- specially Mark Abraham, At the GROMACS compiled with MOPAC 7.0, I tried to simulate my drug, using the QM/MM, at two *.itp files: (a) At the first I put the CHELPG charge fitting. (b) At the second itp file, I put zero charge since all the quantical or semi-empirical methods compu

[gmx-users] Two doubts about GMX!

Hi, GMXers, i've some doubts about the use of GMX and implicit solvent models. I have an huge system ( moreless 10 000 protein atoms) and trying to do MD using explicit solvents but my computer limitations doesn't work very well. 1) someone could help me giving some light in how can i simulate my

[gmx-users] Toplogy file FAD and ADP!

Dear Gmxers, i've trying to develop the topology files for FAD and ADP since the GMX 3.3.1 does not have this molecules. Does someone do it before? I know that FFGMX has one topology of FAD but are the parameters similar for FF53a61 in GMX 3.3.1? Thanks in advance. Samuel Pita. "Do not wear your

[gmx-users] Topolgy file FAD and ADP!

Dear Gmxers, i've trying to develop the topology files for FAD and ADP since the GMX 3.31 odes not have this molecules. Does someone it before? I know that FFGMX has one topology of FAD but are the parameters similar for FF53a61 in GMX 3.3.1? Thanks in advance. Samuel Pita. "Do not wear yourself

[gmx-users] Variable ci problem!

Dear GMXers, I had built my molecular topology "by hand" an when I was minimisate the energy of my system gromacs 3.3.1 give this error message: "Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Step=0, Dmax= 1.0e-02 nm, Epot= -6.12087e+04 Fmax= 1.8

[gmx-users] Variable ci problem!

Dear GMXers, I had built my molecular topology "by hand" an when I was minimisate the energy of my system gromacs 3.3.1 give this error message: "Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Step=0, Dmax= 1.0e-02 nm, Epot= -6.12087e+04 Fmax= 1.8

[gmx-users] Variable ci yet!

Hi all, my problem in my "by hand' topology remains until now but the errors in atoms of solvent added through genbox command at GMX 3.3.1 disappeared. Unfortnately the variable ci is giving me some headaches and because this I cannot do my topology. Can someone help me in this type of problem?

[gmx-users] name of molecules at rtp archives!

Hi GMXers, how can I find the names of the molecules that are represented at rtp archives? I'd tried to see at aminoacids.dat and at *bond.itp but I cannot find the names. For example: ETH, BA, ETHH, RTOL. Which molecules are these? thanks, Samuel Pita. "Do not wear yourself out to get rich;do