HI Francesco,
I did try my best to make RAMD in NAMD fully compatible with the AMBER8 version. So, in principle one should get the same results if running on 1 CPU with exactly the same protocol. The temperature control is very important here.
RAMD is not such a difficult method and therefore I am pretty confident that the AMBEr8 results are reproducible with NAMD. But of course there are other things .. For example, as soon as you'll run in parallel on more than 1 core you'll have differences. As soon as you'll use different temperature control schemes you'll have differences. But this is also the case in standard MD simulations ... So I am not so worried about it in RAMD.
I have to say though we did not publish any work with the NAMD scripts yet. Even the work I'll be publishing soon was done with AMBER8. I did develop the RAMD scripts for NAMD because I didn't want to use AMBER8 anymore. I believe I did enough runs with the NAMD scripts to be confident that they are doing what they are supposed to do. I also have one colleague that hopefully soon will publish some work with these scripts.
So, I do encourage you to use the RAMD scripts for NAMD and if you wish so, compare your runs with runs performed with the AMBER8 implementation. You can download the NAMD scripts with docu and examples from our website: http://projects.villa-bosch.de/mcm/software/namd/
If you encounter any problem, please let me know
Bets wishes
Vlad
-----Original Message-----
From: amber-bounces.ambermd.org on behalf of Francesco Pietra
Sent: Thu 2/11/2010 5:57 PM
To: AMBER Mailing List
Subject: Re: [AMBER] About RAMD
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
> Schloss-Wolfsbrunnenweg 35
> 69118 Heidelberg
>
> Tel: ++49-6221-533202
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]h-its.org
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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Received on Thu Feb 11 2010 - 13:30:03 PST
