[gmx-users] Force Calculation - SBLOCKS

[David van der Spoel]

Mark Abraham wrote:
> Justin M. Shorb wrote:
>> Greetings!
>>
>> I have been running gromacs to simulate a chromophore (NMAd) in water. 
>> I have verified that the coulombic force is calculated correctly by 
>> doing a rerun of the simulation trajectory and extracting the forces 
>> from a forcefield of vanishing force constants (thus removing all vdW 
>> and bonded terms). This works, although it is fairly brute-force.
>>
>> Now, I am trying to scale up and look at a single peptide Amide-I band 
>> in a transmembrane protein. Unfortunately, if I use the same mdp file, 
>> I get different results than if I use the mdp file with which the 
>> production run was generated.
> 
> I don't understand your meaning here.
> 
>> By gmxdump-ing the tpr files, I can figure out the differences between 
>> the run files. I verified that varying PME parameters cause a 
>> negligible effect, and most of the basic I/O parameters of course 
>> shouldn't matter.
>>
>> The biggest difference between the two files is that one reports zero 
>> for the multinr and uses nr=0 and nra=0, whereas the other tpr file 
>> reports 123 for the multinr, nr=123, nra=6326, and then specifies 
>> blocks[SBLOCKS][...]
> 
> Um, no there are huge differences here. One uses temperature and 
> pressure coupling and the other doesn't. One has cut-offs at 1.4nm, the 
> other 1nm. There's many more as well....
> 
> Mark
> 
I agree with mark here. Very different topologies, not just the force 
constants. In addition you do not specify clearly what is the difference 
in result that you observe, i.e. between what and what. PME does not use 
energy groups.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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