[gmx-users] Re: Can I have the mdp file?

Pär Bjelkmar bjelkmar at cbr.su.se
Wed Nov 17 14:06:07 CET 2010


I forward this discussion to the mailing list now because I think that it might be of interest to some people at least. Please find the mdp file of the GROMACS runs attached. To get the energies between GROMACS and CHARMM to match one has to do at least two things:
* make sure the molecular conformation is _exactly_ the same. I.e. the coordinates of the atoms should be identical (inclusive correct number of significant figures)
* run without cut-offs 

Pär Bjelkmar

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17 nov 2010 kl. 13.16 skrev Xin Chen:

> yes, I have done. But the potential calculated by these two methods differs greatly. And the difference between the two is more than 10kj/mol. The CHARMM calculation seems fine. 
> I guess that I set the parameters wrong in the mdp file during the GROMACS calculation...
>> -----Original E-mail-----
>> From: "Pär Bjelkmar" <bjelkmar at cbr.su.se>
>> Sent Time: 2010-11-17 16:18:18
>> To: "Xin Chen" <chenx at mail.ustc.edu.cn>
>> Cc: 
>> Subject: Re: Can I have the mdp file?
>> Hi,
>> I do not fully understand what you're trying to do. To reproduce Table 1 you need to run the program CHARMM as well as GROMACS, have you already done that?
>> /Pär
>> 17 nov 2010 kl. 03.24 skrev Xin Chen:
>>> Professor Bjelkmar:
>>>   hello, I've finished the article that you referred to me in your last mail. It's quite helpful and thank you. But I have some trouble when I test some amoni acid. The results couldn't get well with the table1 in the article. I considered whether I caculated in the same way as you did, especially the mdp options for Gromacs. 
>>>   So, can I have the mdp file when you make the table? The table is also sent as an attachment.
>>>   Thank you and Best Wishes!
>>>                                                         Xin Chen
>>>                                                               2010.11.17
>>> <table1.bmp>

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