Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[Erik Marklund]

Hi,

We are working on a tool for automatic vsite parameter generation, which works 
with most force fields including CHARMM. Stay tuned.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 6 Apr 2018, at 13:11, Anthony Nash 
<anthony.n...@dpag.ox.ac.uk<mailto:anthony.n...@dpag.ox.ac.uk>> wrote:

Hi Stephane,

I hope it is useful. I am afraid I have very little charmm experience. I used 
the approach posted for an amber ff.   I hope someone can help with the charmm 
aspect.

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>
 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>]
 on behalf of ABEL Stephane [stephane.a...@cea.fr<mailto:stephane.a...@cea.fr>]
Sent: 06 April 2018 11:20
To: 
gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Many thanks Anthony

I will read your post blog. I have another quick question: Does the approach 
work by defaults (w/o modifications) for other biomolecules such as surfactants 
or it is necessary to construct a virtual site table as we can found for 
protein in the charmm*.ff distribution ?

Stéphane



--

Message: 3
Date: Fri, 6 Apr 2018 09:33:46 +
From: Anthony Nash 
<anthony.n...@dpag.ox.ac.uk<mailto:anthony.n...@dpag.ox.ac.uk>>
To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>" 
<gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
   virtual interaction sites
Message-ID:
   
<84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk<mailto:84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk>>
Content-Type: text/plain; charset="iso-8859-1"


Hi,

I tried something like this about a year ago and I put an instructional blog 
post together. Warning: it was pulled together from a paper I found and not my 
own efforts although I did get it to work. Any questions I might not be able to 
respond, I'm on vacation!

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane 
[stephane.a...@cea.fr]
Sent: 06 April 2018 08:51
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Hi gmx users,

I know that it is possible to speed up  the simulations by a factor 2 (by using 
a larger timestep) in GROMACS with virtual interaction sites. By I do not find 
a clear procedure on the web in particular if I use CHARMM. Do you have any 
pointers or procedures and examples of mdp files to share with me

Thanks

St?phane

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Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[Viveca Lindahl]

Hi,

There is this ancient gromacs page which I guess you already found:
http://www.gromacs.org/Documentation/How-tos/Removing_fastest_degrees_of_freedom

Here are a couple of references, the second for using virtual sites for
CHARMM lipids:

Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Lindahl, E.
Implementation of the CHARMM force field in GROMACS: Analysis of protein
stability effects from correction maps, virtual interaction sites, and
water models. Journal of Chemical Theory and Computation 6, 459–466 (2010).
Loubet, B., Kopec, W. & Khandelia, H. Accelerating all-atom MD simulations
of lipids using a modified virtual-sites technique. Journal of Chemical
Theory and Computation 10, 5690–5695 (2014).


--
Viveca


On Fri, Apr 6, 2018 at 9:51 AM, ABEL Stephane  wrote:

> Hi gmx users,
>
> I know that it is possible to speed up  the simulations by a factor 2 (by
> using a larger timestep) in GROMACS with virtual interaction sites. By I do
> not find a clear procedure on the web in particular if I use CHARMM. Do you
> have any pointers or procedures and examples of mdp files to share with me
>
> Thanks
>
> Stéphane
>
> --
> 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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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[Anthony Nash]

Hi Stephane,

I hope it is useful. I am afraid I have very little charmm experience. I used 
the approach posted for an amber ff.   I hope someone can help with the charmm 
aspect. 

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane 
[stephane.a...@cea.fr]
Sent: 06 April 2018 11:20
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Many thanks Anthony

I will read your post blog. I have another quick question: Does the approach 
work by defaults (w/o modifications) for other biomolecules such as surfactants 
or it is necessary to construct a virtual site table as we can found for 
protein in the charmm*.ff distribution ?

Stéphane



--

Message: 3
Date: Fri, 6 Apr 2018 09:33:46 +
From: Anthony Nash <anthony.n...@dpag.ox.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
    virtual interaction sites
Message-ID:
<84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"


Hi,

I tried something like this about a year ago and I put an instructional blog 
post together. Warning: it was pulled together from a paper I found and not my 
own efforts although I did get it to work. Any questions I might not be able to 
respond, I'm on vacation!

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane 
[stephane.a...@cea.fr]
Sent: 06 April 2018 08:51
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Hi gmx users,

I know that it is possible to speed up  the simulations by a factor 2 (by using 
a larger timestep) in GROMACS with virtual interaction sites. By I do not find 
a clear procedure on the web in particular if I use CHARMM. Do you have any 
pointers or procedures and examples of mdp files to share with me

Thanks

St?phane

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Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[Anthony Nash]

Hi,

I tried something like this about a year ago and I put an instructional blog 
post together. Warning: it was pulled together from a paper I found and not my 
own efforts although I did get it to work. Any questions I might not be able to 
respond, I'm on vacation!

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/
 

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane 
[stephane.a...@cea.fr]
Sent: 06 April 2018 08:51
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Hi gmx users,

I know that it is possible to speed up  the simulations by a factor 2 (by using 
a larger timestep) in GROMACS with virtual interaction sites. By I do not find 
a clear procedure on the web in particular if I use CHARMM. Do you have any 
pointers or procedures and examples of mdp files to share with me

Thanks

Stéphane

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