Re: [gmx-users] Position restricted md

2007-10-23 Thread Yang Ye
ssage From: sarbani chattopadhyay <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, October 23, 2007 1:35:14 PM Subject: [gmx-users] Position restricted md Hi, I am new to the field of MD.I want to know what is the effectivity of position restricted MD ie. where is th

Re: Re: [gmx-users] Position restricted md

2007-10-23 Thread sarbani chattopadhyay
 I understand.Thank you for the comparative analysis. sarbani On Tue, 23 Oct 2007 Mark Abraham wrote : >sarbani chattopadhyay wrote: >> yes , I had gone through the manual, but is that all? I mean to say that >

Re: [gmx-users] Position restricted md

2007-10-23 Thread Mark Abraham
sarbani chattopadhyay wrote: yes , I had gone through the manual, but is that all? I mean to say that even if the protein suffers from high solvent forces (though the energy minimisation can be done over the whole system ie protein in solvated state) that may not pose much of a problem , in c

Re: Re: [gmx-users] Position restricted md

2007-10-23 Thread sarbani chattopadhyay
 yes , I had gone through the manual, but is that all? I mean to say that even if the protein suffers from high solvent forces (though the energy minimisation can be done over the whole system ie protein in solvated state) that may not pose much of a problem , in case we simulate for suffici

Re: [gmx-users] Position restricted md

2007-10-22 Thread Mark Abraham
sarbani chattopadhyay wrote: Hi, I am new to the field of MD.I want to know what is the effectivity of position restricted MD ie. where is the advantage of doing Position restricted MD.I have a small peptide of 3 reidues.Is it necessary to do a Position restricted MD. What difference will i

[gmx-users] Position restricted md

2007-10-22 Thread sarbani chattopadhyay
  Hi, I am new to the field of MD.I want to know what is the effectivity of position restricted MD ie. where is the advantage of doing Position restricted MD.I have a small peptide of 3 reidues.Is it necessary to do a Position restricted MD. What difference will it make?