[gmx-users] Re: amber parameters in gromacs

[David van der Spoel]

On 2010-07-01 11.19, Rolf Erwin Isele-Holder wrote:
> Hi,
>
> I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, 1-4 interaction, combination rule for LJ, bond length strength, dihedrals, angles) so that they are equal to the parameters used by the other authors with their AMBER FF. The equations uses to calculate the energy are the same, that is why I expected to get the same results. ...so I guess this assumption is not true. Why is it not possible to use these parameters?
>
>
> Is there a way to get a topology of glycerol working with gromacs instead of writing it oneself? I've already tried the Prodrg Server but I didn't get proper results with this topology, either.
>
in order to debug these things you need to compare energies at step 
zero, preferably for one molecule first. IIRC amber does not use the 
factor 1/2 in harmonic potentials, so you would have to multiply the 
force constant by two.

> Regards,
>
> Rolf
>
>
>
> On 07/01/10, Alan<alanwilter at gmail.com>  wrote:
>
>> Hold on, you said *amber*, nevertheless you top has definitions for GROMOS**. Either you are mixing force fields here (which *bad*) or worse, your not using Amber FF, which is *really bad*.
>>
>>
>> I would be helpful if you give the commands you're using for pdb2gmx and grompp. Besides, are you aware of ffamber and acpype? Since you said you have the parameters for glycerol you may not need to build the topology anew, but I do recommend looking at acpype.googlecode.com(http://acpype.googlecode.com) to know more about simulations involving amber ff and gromacs, besides links to important resources like ffamber.
>>
>>
>>
>>
>> Cheers,
>>
>>
>> Alan
>>
>>
>>
>>
>> On Thu, Jul 1, 2010 at 09:13,<gmx-users-request at gromacs.org<gmx-users-request at gromacs.org>>  wrote:
>>
>>
>>
>>>
>>> Dear gromacs-users,
>>>
>>>
>>>
>>> I've been simulating a box of liquid glycerol. The parameter's I have used were taken from an article, whose authors achieved good agreement between their simulation and experiments. These authors used an amber force field and the software ORAC.
>>>
>>>
>>>
>>>
>>>
>>> I used exactly the same parameters as them for my topology and very similar settings in my mdp file. However I did not get the same results as them. Do you know why I get these different results? I am in doubt weather the top of my topology is correct, so I pasted it here:
>>>
>>>
>>>
>>>
>>>
>>>       #define _FF_GROMOS96
>>>
>>>       #define _FF_GROMOS53A6
>>>
>>>
>>>
>>>       [ defaults ]
>>>
>>>       ; nbfunc   comb-rule       gen-pairs       fudgeLJ fudgeQQ
>>>
>>>         1                2               yes             0.5     0.8333
>>>
>>>
>>>
>>>       [ atomtypes ]
>>>
>>>       ;name  at.num   mass      charge  ptype   sigma  epsilon
>>>
>>>          OA     8     0.000      0.000   A      0.3442    0.879228
>>>
>>>          C      6     0.000      0.000   A      0.3816    0.45803592
>>>
>>>          H      1     0.000      0.000   A      0         0
>>>
>>>          HC     1     0.000      0.000   A      0.2774    0.06573276
>>>
>>>
>>>
>>>
>>>
>>>       [ moleculetype ]
>>>
>>>
>>>
>>>       Glycerol      3
>>>
>>>
>>>
>>>       [ atoms ]
>>>
>>>       ;   nr      type  resnr resid  atom  cgnr   charge
>>>
>>>           1         OA     1   GLCR   OAA    1      -0.585    15.9994
>>>
>>>           2         H      1   GLCR   HAA    1       0.396    1.008
>>>
>>>           3         C      1   GLCR   CAD    1       0.182    12.011
>>>
>>>          .....
>>>
>>>
>>>
>>> I think, that by specifying comb-rule = 2 giving sigma and epsilon is correct instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for fudgeQQ are supposed to lower the 1-4 interaction.
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>>
>>> Rolf
>>>
>>
>>
>>
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>
>>
>>>> http://www.bio.cam.ac.uk/~awd28<<


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se