@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
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
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
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
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
to change coordinate of molecule?
but I seems also impossible becasue PME problem!
So whats the solution?
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Friday, April 5, 2013 7:42 PM
Subject: Re: Fw: [gmx-us
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
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