<span class="gmail_quote">Hi!<br>
<br>
Sorry if this message reaches the list twice, but Gmail doesn't let me
know if the list received it... seems that it stores somehow in the
same message if it comes back, so I just know when there are answers. :(<br>
<br>
Anyway, thanks a lot in advance for any help in this subject!<br>
<br>
Yours,<br>
<br>
Jones<br>
<br>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br></span>Hi!<br><br>Well, I was trying to calculate the intermolecular total energy of<br>some long systems here, when I got locked in a problem.<br><br>g_energy allows me to isolate Coulomb-(SR), Coulomb-14 and<br>Coul.-recip. for the coulombic terms, for example. The seems to be
<br>that, in long chain molecules (by long, I mean more than 1-4 maximum<br>distance), the program outputs the 1-n (n>4) intramolecular terms of<br>the interactions together with most of the other intermolecular<br>coulombic terms in Coulomb-(SR) (exception for the molecules so far
<br>that are in the Coul.-recip. part, but my molecules are some times<br>smaller than any cutoff radius used).<br><br>I would like to know if there is any work-around for this, in order to<br>remove the 1-n (n>4) intramolecular terms from the other
<br>intermolecular total energies I get.<br><br>Just in time: I tried to increase, in the topology file, the nrexcl<br>(to 9, the largest number of bonds between two atoms in the molecules<br>simulated) parameter. It helped a lot, and started to yeld really
<br>better values. But, on the other hand, it also yelded very different<br>trajectories, probably due to changes in conformation as a consequence<br>of the lack of forces derived from those intramolecular interactions<br>
it excluded. :(<br><br>Does anybody have any idea of how to deviate from this problem?<br><br>Thanks a lot in advance!<br><br>Jones<br>