Dear Brian and Ross,
Thanks for your answers. Brian, now that you say it, yes, I think that
pmemd gives you some warning about mixing belly and ewald. But since I
need to have atoms really fixed, I was trying to figure out how to use
it anyway. Of course, one has to be really careful when doing this,
but I believe that it can be done.
Ross, yes, I know that PME is not pairwise decomposable, but what I
don't understand is why in the bonded terms fixed atoms are not
included. That causes EELEC and 1-4EEL to be incompatible. In other
words, wouldn't be better to have all terms (fixed and not fixed)
included in the energy, just as we do when using ntr?
Anyway, to make sure that what I am doing is correct, I need somebody
to check what I said in the previous e-mail. I imagine that anybody
who was involved in the coding of the energy part has to know if what
I say is right or not.
Thanks,
Ignacio
On Thu, Jul 28, 2011 at 4:03 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Ignacio,
>
> I believe the problem you describe is a function of the fact that the PME
> terms are not pairwise decomposable and thus it is not possible to remove
> the contribution between fixed atoms when using Belly. The general advice is
> that one should NOT be using belly with PME/Ewald calculations. Instead it
> is better to use ntr=1 harmonic restraints.
>
> Others may be able to provide more in depth comments.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Ignacio J. General [mailto:ijgeneral.gmail.com]
>> Sent: Thursday, July 28, 2011 12:49 PM
>> To: AMBER Mailing List
>> Subject: [AMBER] Energy output when using ibelly
>>
>> Dear Amber users:
>>
>> After experimenting a little with Belly using Ewald, I found something
>> I didn't expect about the MD output energies. Could anybody please
>> check that what I understand is correct?
>>
>> In the standard output there are, among several other quantities, one
>> called EELEC and another called 1-4EEL. The 1st one gives the total
>> Ewald electrostatic energy of the system, with the exception of the
>> 1-2, 1-3 and 1-4 interactions (or are those terms also included?). The
>> 2nd one gives a 1-4 electrostatic energy, calculated outside Ewald, I
>> imagine in the same way that the others (BOND, ANGLE, etc.) are
>> calculated. So that if you put together EELEC + 1-4EEL, you get the
>> total electrostatic energy of the whole system (of course, except 1-2
>> and 1-3 interactions).
>>
>> So far, so good. But I found out that if you use belly, then the
>> 1-4EEL (along with BOND, ANGLE, etc.) ignore the energies between
>> fixed atoms. On the other hand, the Ewald calculation, and thus EELEC,
>> is unaffected by belly, so that energy does include even the fixed
>> atoms. So EELEC and 1-4EEL are incompatible! Consequently, if we do
>> EELEC + 1-4EEL, we don't get the total electrostatic energy of the
>> system.
>>
>> This could not be a problem, depending on what you are calculating. In
>> particular, if you do charge TI, DV/DL is obtained from (EELEC +
>> 1-4EEL), so you may have big problems here...
>>
>> If anybody has some comment on this I would really appreciate it.
>>
>> Ignacio
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 28 2011 - 13:30:04 PDT
