Re: [gmx-users] Gromacs with QMMM Support

yes, that's right ;) Quoting Jack Shultz : I am reading this page http://wwwuser.gwdg.de/~ggroenh/qmmm.html Is it correct to assume you need one of the following to compile Gromacs with QMMM support? Gaussian GAMESS-UK MOPAC7 or mopac7.tar.gz -- Jack http://drugdiscoveryathome.com http://hy

Re: [gmx-users] gmx-users Digest, memory allocation error

hi justin,thanks for your replyTotally I have 6126 atoms (residues + DPPC ) I am using the same pdb file and lipid pdb (DPPC128) which is given in the KAPL tutorial.E ven tried it without adding any solvents to it, I am getting the same error (memory allocation).My system has 15.6 GB free space

[gmx-users] Gromacs with QMMM Support

I am reading this page http://wwwuser.gwdg.de/~ggroenh/qmmm.html Is it correct to assume you need one of the following to compile Gromacs with QMMM support? Gaussian GAMESS-UK MOPAC7 or mopac7.tar.gz -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list

Re: [gmx-users] RMSD Vs Residue no by Grace

Hi, RMSD is given at a specific time, so you can ran g_rms for each residue (create index file witha specific residue in) and then take the RMSD of each residue at time T and plot it. But I think you should look into g_rmsf, this might fit you better, although it calculate the fluctuations rather

Re: [gmx-users] An unexpected behavior of rdf calculated by the g_rdf command

Dear Justin:   Thank you very much for you advise, it seems I should read the manual more carefully. The Au and Cl atoms are formed a cluster [AuCl4]- and there are bonds between Au and Cl.   Thank you again for your help.   

[gmx-users] free energy calculations using MBAR and gromacs

Hi, I am trying to calculate free energy of a system that involves disappearance of LJ particle at lambda=1 in explicit solvent. I ran the simulation at 20 different lambda points ranging from 0 to 1, using soft core potential. In order to use MBAR method (python implementation from Michael shirt

Re: [gmx-users] gromp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

Yirdaw, Robel Birru wrote: Dear gromacs users, I have been attempting to test my new gromacs installation of version 4.0.5. using gmxtest 4.0.4 but I keep getting the following error message: ERROR: Can not find grompp in your path. Please source GMXRC and try again. I have sourced the GMXRC f

Re: [gmx-users] Tabulated potentials make newbies crazy

ms wrote: Dear Mark, First of all, thanks for your patient and thorough reply! Mark Abraham ha scritto: Yeah, that's an unfortunate fact of life. The manual can't be organized so that everybody finds all the information they want in one location with the detail they need right now. Using tabul

Re: [gmx-users] RMSD Vs Residue no by Grace

rituraj purohit wrote: Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? g_rm

Re: [gmx-users] Tabulated potentials make newbies crazy

ms wrote: Sorry to say I can't help with the larger problem, but I'd like to comment on this: The problem is that since I have a single molecule now, and the single molecule must be neutral, so it must be all a single charge group ("Therefore we have to keep groups of atoms with total char

[gmx-users] RMSD Vs Residue no by Grace

Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? looking forward for u r important sugg

Re: [gmx-users] Tabulated potentials make newbies crazy

Dear Mark, First of all, thanks for your patient and thorough reply! Mark Abraham ha scritto: > Yeah, that's an unfortunate fact of life. The manual can't be organized > so that everybody finds all the information they want in one location > with the detail they need right now. Using tabulated po

Re: [gmx-users] how can i coarse grained the protein atomic structure

nafiseh farhadian wrote: Dear User, i simulated the lysozyme protein in atomic level and now i'm going to coarse grained it. i'm working with Martini's filester. but i don't know how can i coarse grained my atomic.pdb file to cg.pdb? is there anyone who could help me? Please refer to t

Re: [gmx-users] Tabulated potentials make newbies crazy

ms wrote: Hi, I am really having a hard time figuring out how to use tabulated potentials correctly. In general, the information on how to use tables is sparse and scattered in several points of the manual (ch.5, ch.7, ch.6.7...) -I hope to write a short howto in the wiki once I get this workin

[gmx-users] how can i coarse grained the protein atomic structure

Dear User, i simulated the lysozyme protein in atomic level and now i'm going to coarse grained it. i'm working with Martini's filester. but i don't know how can i coarse grained my atomic.pdb file to cg.pdb? is there anyone who could help me? Regards, -- gmx-users mailing listgmx-users@grom

Re: [gmx-users] Charge groups & Coulomb switch - artifacts in radial distribution function. Atom-based or group-based truncation?

Will Glover wrote: Hi, I have constructed a gromacs MD simulation of liquid tetrahydrofuran (at RTP) in which I'm treating each molecule as a charge group. When using a Switch for both the Coulomb and VdW interactions I see artifacts in the radial distribution function of the Oxygen--alpha-ca