[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 1

[Marzieh Saeedi Masineh]

Dear Michael and all ,
I want to simulation drug in water as well as drug in water and octanol (saturated octanol phase) to determine free energy of drug in water and oil phase to calculate partition coefficient of drug, but the parameters for expanded ensemble simulation that I said (the integrator, t coupl, pcoupl, and constraint-algorithm were set to md-vv, Nose-Hoover, MTTK and shake, respectively) are not in good combination and my runs were crashed. Any suggestion about these parameters are welcome.    

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Today's Topics:

   1. Expanded ensemble error (Marzieh Saeedi Masineh)
   2. Re: Expanded ensemble error (Michael Shirts)
   3. Re: Expanded ensemble error (Michael Shirts)


----------------------------------------------------------------------

Message: 1
Date: Sat, 30 Apr 2016 18:07:37 +0430 (IRDT)
From: Marzieh Saeedi Masineh <msaeedi at mail.kntu.ac.ir>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Expanded ensemble error
Message-ID:
	<1508594146.23093.1462023457470.JavaMail.zimbra at mail.kntu.ac.ir>
Content-Type: text/plain; charset=utf-8

Dear Gromacs users, 
I wanted to use expanded ensemble for calculating solvation free energy of a drug molecule in the water based on "Ethanol solvation with expanded ensemble in gromacs". in this example the integrator, t coupl, pcoupl, and constraint-algorithm were set to md-vv, Nose-Hoover, MTTK and shake, respectively. When I used these parameters in Gormacs 4.6, I faced an error related to the shake algorithm:(SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS) 
I tried different options for these parameters, but I my runs were crashed. Can any person help about the exact combination of these parameters ( the integrator, t coupl, pcoupl, and constraint-algorithm) that works properly. it is noted that, I searched in the mailing list, but i didn't find any answer about it. Thanks in advance. 



------------------------------

Message: 2
Date: Sat, 30 Apr 2016 11:48:51 -0600
From: Michael Shirts <mrshirts at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: "gromacs.org_gmx-users"
	<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Expanded ensemble error
Message-ID:
	<CA+zJb=jXbWww8eeEFLF0OgHJpLJ7AVsgttNGGosvg6cB+Ps=yA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

If you are doing solvation in water, I would suggest not bothering
with expanded ensemble. I would just use standard molecular dynamics
at a range of lambda values.  We have some information that it can be
useful with binding problems, but with solvation alone, you are
probably just fine running a series of alchemical simulations in
parallel.  The expanded ensemble simulations don't really help
sampling that much.

We have recently done some expanded ensemble simulations with drug
binding, and we will try to put a tutorial in the next couple of
months.  There are some subtleties that can cause problems.

On Sat, Apr 30, 2016 at 7:37 AM, Marzieh Saeedi Masineh
<msaeedi at mail.kntu.ac.ir> wrote:
> Dear Gromacs users,
> I wanted to use expanded ensemble for calculating solvation free energy of a drug molecule in the water based on "Ethanol solvation with expanded ensemble in gromacs". in this example the integrator, t coupl, pcoupl, and constraint-algorithm were set to md-vv, Nose-Hoover, MTTK and shake, respectively. When I used these parameters in Gormacs 4.6, I faced an error related to the shake algorithm:(SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS)
> I tried different options for these parameters, but I my runs were crashed. Can any person help about the exact combination of these parameters ( the integrator, t coupl, pcoupl, and constraint-algorithm) that works properly. it is noted that, I searched in the mailing list, but i didn't find any answer about it. Thanks in advance.
>
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> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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------------------------------

Message: 3
Date: Sat, 30 Apr 2016 11:48:51 -0600
From: Michael Shirts <mrshirts at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: "gromacs.org_gmx-users"
	<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Expanded ensemble error
Message-ID:
	<CA+zJb=jXbWww8eeEFLF0OgHJpLJ7AVsgttNGGosvg6cB+Ps=yA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

If you are doing solvation in water, I would suggest not bothering
with expanded ensemble. I would just use standard molecular dynamics
at a range of lambda values.  We have some information that it can be
useful with binding problems, but with solvation alone, you are
probably just fine running a series of alchemical simulations in
parallel.  The expanded ensemble simulations don't really help
sampling that much.

We have recently done some expanded ensemble simulations with drug
binding, and we will try to put a tutorial in the next couple of
months.  There are some subtleties that can cause problems.

On Sat, Apr 30, 2016 at 7:37 AM, Marzieh Saeedi Masineh
<msaeedi at mail.kntu.ac.ir> wrote:
> Dear Gromacs users,
> I wanted to use expanded ensemble for calculating solvation free energy of a drug molecule in the water based on "Ethanol solvation with expanded ensemble in gromacs". in this example the integrator, t coupl, pcoupl, and constraint-algorithm were set to md-vv, Nose-Hoover, MTTK and shake, respectively. When I used these parameters in Gormacs 4.6, I faced an error related to the shake algorithm:(SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS)
> I tried different options for these parameters, but I my runs were crashed. Can any person help about the exact combination of these parameters ( the integrator, t coupl, pcoupl, and constraint-algorithm) that works properly. it is noted that, I searched in the mailing list, but i didn't find any answer about it. Thanks in advance.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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