[gmx-users] query for g_sas

x27;t used 3.3.1 or 3.3.2. So what is the update in this front.Previous people who have gone through this, please help me out. Finally I also read in the list about the flexibility of chossing the "VDW radii" options. Has anything been done yet? Thank you. -- Dilraj Lama, Gradua

[gmx-users] TFE query

the simulation using "g_energy".The average vaules for the properties are as: Temperature: 300.67 Density: 1402.95 Pressure: -2.59 Is the density value reasonable??? Why is the pressure value so different? I would be very greatfull If I could get some suggestions on the param

Re: [gmx-users] Generating a solvent box

of the TFE molecules. But what I want to do now is to have a predfined cubic box dimension which I want to solvate with a fixed number of TFE molecules corresponding to a given density. Thanks for your response. > Quoting Dilraj Lama <[EMAIL PROTECTED]>: > >> Hello gmx users, &g

[gmx-users] Generating a solvent box

" and "genconf" for the purpose but am not able to achieve my aim.If someone has tried to do this before and have some idea, I would be thankfull if you could shed some light on the subject. Thanking you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab

[gmx-users] query regarding methanol density

ted by Bert de Groot. I have set up system with the peptide solvated in a cubic methanol box.The density of the sysytem is now reported to be about 764.677 g/l.My query is, is it ok for me to perform the simulation with the mentioned density?? Thank you all. -- Dilraj La

Re: [gmx-users] Restart

g/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 -

[gmx-users] Generalized order parameter S2

e appropriate? Also using "g_rotacf" I am still not very clear on how to go about using the tool. Can anyone who has previuosly performed this calculation help me out. I look forward to your responses. Thank you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simu

[gmx-users] References for globular protein simulation using PME

Dear all gmx-users, I have been trying to dig out some well cited paper on simulation of globular protein using PME .Can anyone please suggest to me some references I can look out for. Thanks to all. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular

Re: [gmx-users] defining 2 posres at a time in mdp

cs.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 > -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecula

[gmx-users] Installation problem in IBM pawer PC

for stdint.h... yes checking for unistd.h... yes checking for int... yes checking size of int... configure: error: cannot compute sizeof (int), 77 See `config.log' for more details. -- Dilraj Lama, PhD Student, c/o Dr. R. Sankararamakrishnan, Bioinformatics and Biomolecular Simulation Lab, Dept

[gmx-users] Installation problem in IBM pawer PC

compute sizeof (int), 77 See `config.log' for more details. -- Dilraj Lama, PhD Student, c/o Dr. R. Sankararamakrishnan, Bioinformatics and Biomolecular Simulation Lab, Dept. of BSBE,IIT-Kanpur, UP-208016:India email:[EMAIL PROTECTED];[EMAIL PROTECTED] mob:09415473973 biny2K5830YeC.bin