Re: Fw: [gmx-users] water molecule can not be settled

2013-04-08 Thread Anirban
@yahoo.com] > Sent: Friday, April 05, 2013 5:22 PM > To: Discussion list for GROMACS users > Subject: Re: Fw: [gmx-users] water molecule can not be settled > > You mean start over the NPT step? > > > > Sincerely, > Shima > > > - Original Message - > Fr

RE: Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Luis Felipe Pineda de Castro
water molecule can not be settled You mean start over the NPT step? Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, April 5, 2013 7:50 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at

Re: Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Justin Lemkul
On Fri, Apr 5, 2013 at 11:22 AM, Shima Arasteh wrote: > You mean start over the NPT step? > > Yes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://w

Re: Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Shima Arasteh
You mean start over the NPT step?   Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, April 5, 2013 7:50 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh

Re: Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Justin Lemkul
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh wrote: > As I visualized the system, I see a water molecule somewhere between lipid > chains near the protein entrance. This has been happen during NPT. I' d > like to delete this molecule but with such a kind of fatal error this would > impossible. S

Re: Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Shima Arasteh
ers] water molecule can not be settled On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh wrote: I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? > > It's unlikely that some ad hoc change will magically fix a problem.  Energy min

Re: Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Justin Lemkul
On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh wrote: > I' d like to know if it is acceptable to change the molecule coordinates > to solve this problem? > > It's unlikely that some ad hoc change will magically fix a problem. Energy minimization should take care of clashes. > Some time back, I

Fw: [gmx-users] water molecule can not be settled

2013-04-05 Thread Shima Arasteh
I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent. Would you please give me suggestions? I need them urgently.