[gmx-users] Mutagenesis

ement, but as a check of the feasibility of the complex)? Does anyone have a better/easier way to do this? Thanks a lot for your help, Esther -- Esther Caballero-Manrique Unit of Cancer Pathology Center for Excellence in Research on Aging University "G. D' Annunzio" Via Colle de

Re: [gmx-users] surface area

_ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -

Re: [gmx-users] Using g_energy in a noninteractive mode script

Hector, You could use bash to choose your option, i.e., g_energy <<< "yourchoice" Esther [EMAIL PROTECTED] wrote: Dear Users, I'm constructing a script to analize my dynamics. I need to run g_energy for some of these analisis. I set everything to run without intera

Re: [gmx-users] Free energy calculations

http://md.chem.rug.nl/education/Free-Energy_Course/index.html http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial Both very "decent". Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR (USA) Viswanadham Sridhara wrote: Hello gmx

Re: [gmx-users] Viscosity in PE

. Hope it helps, Esther Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR usa 541-346-2485 Alessandro Mattozzi wrote: Dear Gromacs-users I have already run some MD, both in NVT and NPT, of Polyethylene (1000 atoms-backbone). I would like to estimate the viscosity of my syst

Re: [gmx-users] theory of MD

[EMAIL PROTECTED] wrote: Dear all, My question is on the theory of MD. I actually could not find any material which describes in detail about the time integration algorithm. 1) I wanted to know why the time integration algorithm has to be used, I mean the practical benefits of it. I want the

Re: [gmx-users] Hen egg white lysozyme.

ribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Esther Caballero-Manrique Graduate Teaching Fellow Chemistry Department 1253 University of Oregon Eugene,

Re: [gmx-users] Attempting small molecule . . .

d be appreciated. > > Regards, Marc > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to t

Re: [gmx-users] Variable ci problem!

don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Esther Caballero-Manrique Graduate Teaching Fellow Chemistry Department 125

Re: [gmx-users] Toplogy file FAD and ADP!

ts/users.php I have it for ADP, from the PRODRG server, would you like me to send you the file? -- Esther Caballero-Manrique Graduate Teaching Fellow Chemistry Department 1253 University of Oregon Eugene, OR 97403 (USA) 1-541-346-2485 ___ gmx-users

Re: [gmx-users] Re: question about files

Have you followed the Drug-Enzime complex tutorial found at http://www2.umdnj.edu/~kerrigje/structbio_II.htm ? On Fri, 09 Jun 2006 20:40:28 +0200, David van der Spoel <[EMAIL PROTECTED]> wrote: > Robson Pacheco wrote: > > Dear Sirs > > > > I am new in molecular simulations, and I am experiencin

[gmx-users] Free energy of conformation

in the top file (which goes from avge -90 to 90), but I am thinking that maybe there are other things that I need to account for. Any ideas …? Thanks!! Esther Caballero-Manrique Graduate Teaching Fellow Chemistry Department 1253 University of Oregon Eugene, OR 97403-1253 (541

[gmx-users] Conformation free energy

amino acid calculation, I am wondering if there is a more obvious way to do this that I've overlooked? And if there isn't, what is the path to go from conformation 'A' to conformation 'B' in the top file? Thanks in advance for your help, Esther Esther Caballer