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Inte command
#16371 11/29/07 02:33 PM
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marcin Offline OP
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Hi,
I wanted to calculate an energy of a residue in a protein (the residue belongs to the protein). By this I mean internal energy of a residue + interaction energy between the residue and the rest of the protein.
I did it in two different ways:
1. inte sele segid prot .and. ires 2 end sele segid prot end
2. a loop of:
inte sele segid prot .and. ires 2 end sele segid prot .and. ires (1->end_of_protein) end
and then summed up energies of all pairwise calculations

I thought that reults of 1 and 2 should be the same but they are not, except for the first residue.

Could you explain why?
I checked and energy1 is not equal to energy2 - internal energy of a residue, or to half of the difference.

By the way I'm using param19_eef1, where nonbonded interactions are calculated by groups, but according to the manual inte works for groups.

Any comments welcome

Thank you in advance
marcin

Re: Inte command
marcin #16372 11/29/07 07:49 PM
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The answer is probably somewhere in the middle of this thread:

http://www.charmm.org/ubbthreads/showfla...h=true#Post4592

Re: Inte command
jb007 #16373 11/30/07 10:43 AM
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Hi Johan,

Thanks for your answer.
However, I'm still a bit confused. I read the thread you indicated and I think my problem is slightly different from the problems described there (correct me if I'm wrong).
Cesar (cmp_fc2) didn't include cross-term (sidechain vs backbone) and this was the reason for discrepancy.
You found a small difference for coulomb term due to roundoff errors.

I think my problem is still a bit different (I'm interested in nonbonding terms only).
In my first calculation (inte sele segid prot .and. ires 2 end sele segid prot end) I have 8 atoms in the first selection and 1953 (the whole protein including res2) in the second selection.
In my second calculation I always have 8 atoms in the first selection and a variable number of atoms in the second selection (depending on the residue chosen). But a number of atoms in the second selection sums up to 1953 if I loop the second calculation over all residues (inluding res2).

Inte works by calculating pairwise calculations between all atoms in one selection against all atoms in the second selection and summing them up(is this right?). It should not matter if charmm does the summation (as in my 1st calculation), or if I do it myself (as in 2nd calculation). I'm using groups, but it shouldn't be a problems, because groups are always fully included in a residue, so in the 2nd calculation I don't cut through groups.

The difference between calculation one and two is bigger than roundff errors. For example for res3:
elec vdw eef1
1. calc: -20.25003 -15.36342 16.50047 3
2. calc: -31.2878 -17.2872 19.7074 inte3.out

So what is the reason for this difference?

Thank you for your time
marcin

Re: Inte command
marcin #16374 12/05/07 05:21 PM
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i checked and - as you correctly stated - the energies should be the same for either approach:

1. inte sele ( segid pxt1 .and. ires 2 ) end sele segid pxt1 end

energy: -15.5004

2. (looping)
inte sele ( segid pxt1 .and. ires 2 ) end sele ( segid pxt1 .and. resid @i ) end

total sum of non bonded energy between residue pairs:
energy : -15.5003

used the standard 22 force-field with no other terms than the elec and vdw (just default settings), so perhaps the issue is related to the eef1 part?

This can easily be checked by turning all but the non bonded energies off - i.e. "skipe all excl elec vdw".

Last edited by jb007; 12/05/07 10:15 PM.

Moderated by  BRBrooks, John Legato 

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