[gmx-users] Editing the functions of amber

[Asaf Farhi]

Thank you very much.
Have a nice weekend,
Asaf
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Thursday, March 22, 2012 5:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Editing the functions of amber

On 23/03/2012 2:56 AM, Asaf Farhi wrote:
> Thank you very much for the reply.
> I tried to send this question few days ago and they said that I'm not allowed to post there.
> (The edition of the replica exchange shouldn't be complicated.)
> Do you have any tips regarding what I should do?

Read the RE documentation the manual and mdrun -h. Get out a debugger
and step through the code. Most of the stuff relevant to replica
exchange is in src/kernel/repl_ex.c

Mark

>
> Thanks in advance,
> Best regards,
> Asaf_
> _______________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
> Sent: Thursday, March 22, 2012 5:06 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Editing the functions of amber
>
> On 23/03/2012 1:59 AM, Asaf Farhi wrote:
>> Dear Matt
>>
>> Thank you very much for the reply.
>> About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy.
>> Can this be done with the table lookups?
> Yes, any potential that is a function of distance between pairs can be
> done. See manual 6.7.2. Of course, plain cut-offs can be done without
> tables since about 1976...
>
>> Are you willing to cooperate with us on 2?
> I don't have time for new projects, but a post to gmx-developers may
> elicit feedback on feasibility.
>
> Mark
>
>> Thanks
>> Best regards,
>> Asaf
>>
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
>> Sent: Thursday, March 22, 2012 4:24 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Editing the functions of amber
>>
>> On 23/03/2012 12:50 AM, Asaf Farhi wrote:
>>> Dear Matt
>>>
>>> Thank you very much for your reply.
>>> The things we want to change are the following:
>>> 1. Introduce a cutoff energy in the Van Der Waals and electrical potential.
>>> 2. Editing the replica exchange function.
>>> 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials).
>> Probably you can do 1 and 3 with table lookups - see manual.
>>
>> Mark
>>
>>> In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article).
>>>
>>> Thank you very much,
>>> Best regards,
>>> Asaf
>>>
>>> ________________________________________
>>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Matthew Zwier [mczwier at gmail.com]
>>> Sent: Tuesday, March 20, 2012 8:15 PM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] Editing the functions of amber
>>>
>>> Dear Asaf,
>>>
>>> I think we need significantly more information in order to help you.
>>> What function are you trying to port?  What are you trying to do with
>>> it (that is, what is the scientific question you're trying to answer)?
>>>
>>> GROMACS is a clean codebase, and remarkably easy to read for how much
>>> computer science goes into it. However, there will likely be a
>>> relatively severe impedance mismatch between the AMBER and GROMACS
>>> code.  AMBER is written primarily in FORTRAN, and GROMACS is written
>>> entirely in C.  Data (like topology and coordinates) are stored
>>> differently in each code.  Finally, GROMACS uses a lot of specialized
>>> techniques to speed up computations (table lookups instead of function
>>> calls, and the like), so implementing an algorithm in GROMACS is often
>>> more about re-expressing the algorithm in GROMACS style than it is
>>> about simply transliterating a routine from FORTRAN into C.
>>>
>>> What you're proposing is likely to be almost as formidable a task as
>>> implementing an algorithm from scratch based on the original papers.
>>> That said, our group has had success with modifying GROMACS code in
>>> the past, and it turned out to be an efficient solution.
>>>
>>> Cheers,
>>> Matt Zwier
>>>
>>> On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhi<asaf.farhi at weizmann.ac.il>    wrote:
>>>> Dear Gromacs User
>>>>
>>>> Hi.
>>>> My name is Asaf and I'm trying to edit one of the functions in amber in
>>>> order to use it in GROMACS.
>>>> I wanted to ask if anyone knows how to do it?
>>>>
>>>> Thanks in advance,
>>>> Best regards,
>>>> Asaf
>>>>
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