[gmx-users] testing Tip5p water

Dear all, a similar problem was proposed in this list in 2002: http://www.gromacs.org/pipermail/gmx-users/2002-August/002339.html I cannot solve my problem, when testing tip5p in gromacs. T( c) density((g/cm^3) -E(kcal/mol) REF125.0 0.999

RE: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

center of mass > motion. Thanks for clarification. > For a system with freeze group, we should not use any removal of com motions, and this system should still work. I don't find this relevant descriptions in gmx-manual, and it may be added into it. Yusong > > > > tuyuson

RE: [gmx-users] how to make choices of COM in the system with freeze group?

> > You can opt for 3). > > If your system only compose of nanotube and water, why freeze it? Thank Yang Ye, we are doing some tests on effects of T-coupling caused by removing COM in the system with freeze groups Regards, Yusong > > tuyusong wrot

RE: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 4:01 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong wrote: > Even in the system with position-restrain, when only removing com of SOL > group, gm

RE: [gmx-users] Warning message with 3.3.3 but not with 3.3.1

Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] O

[gmx-users] how to make choices of COM in the system with freeze group?

Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of "system" as a who

[gmx-users] how to make choices of COM in the system with freeze group

Hi, Users, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 2) only remove the COM of "system" as a whole. How