[gmx-users] REMD and demux.pl

Hi Gmx-users, i tried downloading the demux.pl script from the CVS repository. but i can't get thru, could anyone plz email me the script or just post it as a reply to this request, that would be a great help. thanks. arindam -- Arindam Ganguly Graduate Student VP(Chemistry Graduate St

[gmx-users] REMD and demux.pl

suggest any resource or tutorial for understanding the concepts and fundamental of running and performing molecular dynamics calculations in a cluster computing environment. thanks very much for your help. Arindam Ganguly ___ gmx-users mailing listgmx

[gmx-users] REMD and demux.pl

Hi Gmx-Users, i am trying to run REMD for a protein, i looked at the mailing list regarding the discussion of REMD. it looks like veryone talking about the demux.pl perl script. i can;t find that in gromacs directory. can anyone plz provide me with the exact path of the script. i also checked the

[gmx-users] g_confrms_d options

Hi David,thanks again for the explanation. it makes a lot of sense now. any particular reference/s comes to your mind one should go thru regarding the same topic. it would really be a greta help. and thanks again. Arindam Ganguly ___ gmx-users mailing

[gmx-users] g_confrms_d options

Hi David,Thanks for the reply. very well i agree with what you have to say. however in that case the answer  which i am getting for other options claiming that the lsq fit say for backbone is 0.98732 so on ., are useless values. now again if that is the case shoukld i assume that native structure R

[gmx-users] g_confrms_d options

his error message in other options. is there really problem here or i am missing something. pzl help thanks. Arindam Ganguly ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post

[gmx-users] g_confrms_d

Hi Gmx-users in the manual of GROMACS 3.3 for the g_confrms , the manual states the following.   " g confrms computes the root mean square deviation (RMSD) of two structures after LSQ fitting the second structure on the first one. " anybody has references to LSQ method ? thanks very muc

[gmx-users] Beta Sheet folding simulation

Hi gmx-users,has anybody done a Beta Sheet folding simulation. any tutorials, references, books, input parameters, i hope i am not aksing for too much. i need help. i read thru gromacs manual and it talks about REMD. that's all. so need some more inputs from all of you out there. thanks. ar

[gmx-users] *.xvg to jpeg/pdf/png

Hi gmx-users,i have a energy.xvg file, but i am not able to convert it to a jpeg, pdf or png format. in fact any cross platform format so that i can print out or send it for publications. any help in this regard is welcomed. thanks. arindam ___ gmx-users

[gmx-users] generate a pdb file

Hi GROMACS users,i have a 20 Amino acids peptide. i know the sequence. could you tell me how to generate a pdb file for the same so that it can be used for MD simulations using GROMACS. thanks.Arindam ___ gmx-users mailing listgmx-users@gromacs.org h

[gmx-users] g_energy_d

Hi All,i am using the g_energy command to look for the info in simulation, when i give the command this is what is get :-bash-2.05b$ g_energy_d :-)  G  R  O  M  A  C  S  (-:    God Rules Over Mankind, Animals, Cosmos and Such     :-)  VERS

[gmx-users] POPC simulation

Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly ___ gmx-users mailing list

[gmx-users] POPC simulation

remains and it say again "LC3" atomtypes not found. so me still stuck. plz help. thanks. arindam ganguly On 5/24/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World

[gmx-users] POPC simulation

Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just app

[gmx-users] POPC simulation

Hi Steffen,Thanks very much for the prompt reply. i made the changes as mentioned such that my popc.top looks like this :-#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp" #include "ffgmx2nb.itp"#include "ffgmx2bon.itp"however is still get the same message "Fatal error: Bonded/nonbonded a

[gmx-users] POPC simulation

Hi gmx-users,i am trying to run a POPC simulation. this is what i have done. i downloaded the popc128apdb, lipid.itp , popc.itp files from the following website http://moose.bio.ucalgary.ca/index.php?page=Downloads then i also downloaded the ffgmx_lipids files from the gromacs website.i have copie

[gmx-users] Villin Benchmarks grompp error (Please Help)

Hi GROMACS users,sorry please disregard the earlier message realised it was too long.i am new to GROMACS. i have been trying to run the Villin Benchmarks using the conf.gro, grompp.mdp and topol.top file provided with the benchmark folder. i giving the grompp command as follows grompp -f grompp.mdp