[gmx-users] query for g_sas

the flexibility of chossing the VDW radii options. Has anything been done yet? Thank you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973

[gmx-users] TFE query

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 parameters and on the values of the properties mentioned. Thank you. -- Dilraj Lama, Graduate student

[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, Dept. of BSBE;IITK

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, I have

[gmx-users] query regarding methanol density

. 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 Lama, Graduate student

Re: [gmx-users] Restart

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 -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur

[gmx-users] Generalized order parameter S2

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 Simualtion lab, Dept. of BSBE;IITK-kanpur

[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

)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 Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email