Re: [gmx-users] settle issue

2008-07-29 Thread Yang Ye
David van der Spoel wrote: Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical

RE: [gmx-users] settle issue

2008-07-29 Thread Mu Yuguang (Dr)
/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, July 29, 2008 2:27 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] settle issue Mu Yuguang (Dr) wrote: > Dear All, > When I try to simulate T

Re: [gmx-users] settle issue

2008-07-28 Thread David van der Spoel
Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-mo

[gmx-users] settle issue

2008-07-28 Thread Mu Yuguang (Dr)
Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and se