Hi Vlad:
Although I have Amber8 implementing ramd, I am interested in trying
ramd with namd because I have problems in setting up the files needed
for amber, an issue that has nothing to do with ramd. Therefore, how
far was ramd tested with namd? Did you carry out comparisons with
ramd-amber8?
thanks
francesco pietra
On Thu, Feb 11, 2010 at 3:57 PM, Vlad Cojocaru <Vlad.Cojocaru.h-its.org> wrote:
> Hi Gokul,
>
> RAMD is not implemented in AMBER10. It was originally implemented in AMBER8.
> Afterwords, between AMBER8 and AMBER9 some major changes occurred and there
> was nobody in the group to be good in FORTRAN. Therefore, the patch was not
> ported.
>
> Of course it would be great if somebody would port it to AMBER10. And it
> would be even nicer if it would be distributed with AMBER in the future. But
> as I am poor in FORTRAN, I do not plan to do anything on that. We also do
> not have anybody else who can do that.
>
> In the meantime, I implemented RAMD in NAMD and I believe it will be
> included in the 2.7 stable release of NAMD. The scripts for running RAMD in
> NAMD with documentation and examples may be downloaded on our website
> (http://projects.villa-bosch.de/mcm/software/namd/). In principle, they may
> be run with any version of NAMD.
>
> If you decide to go on and port RAMD to AMBER10, we can offer support in
> terms of testing, comparing with older results (the ones we have experience
> with) and so on ...
>
> Best wishes
> Vlad
>
>
> gokul algates wrote:
>>
>> Dear All
>> I have an amber 10v package. i would like to patch RAMD but it is
>> available only for amber 8. Is that RAMD is implimented in amber 10. or any
>> other way to patch RAMD
>> Thanking you
>> E R Azhaigya singam
>>
>>
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>>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> Heidelberg Institute for Theoretical Studies
> HITS gGmbH
> Molecular and Cellular Modelling Group
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> 69118 Heidelberg
>
> Tel: ++49-6221-533202
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]h-its.org
>
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>
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Received on Thu Feb 11 2010 - 09:00:02 PST
