Hi Ge,
Im not a PME expert, but maybe what you see is more like a shifting of the
(arbitrary) EEL zero point with a different cutoff. I think it would be
more meaningful to compare the forces you get with the different cutoffs,
which is what would lead to different dynamics and hence different results
of your MD.
Kind Regards,
Thomas
On Tue, Aug 20, 2024 at 3:44 PM Ge Song via AMBER <amber.ambermd.org> wrote:
> **Warning** The sender address (Ge Song via AMBER ) can not be verified,
> sender email address could be spoofed. Please take care to proceed.
> Dear community,
>
> In sander, it performs PME for calculation of electrostatic interaction in
> periodic system, and the 'cut' keyword is used only for the cutoff of
> direct space summation. Therefore, in principle, setting it as 8 Angstrom
> or 10 Angstrom won't significantly change the EEL energy in the output,
> this is also in a previous discussion at here RE: Re: [AMBER] cutoff from
> Ross Walker on 2010-06-05 (Amber Archive Jun 2010) (ambermd.org)<
> http://archive.ambermd.org/201006/0138.html>. On the other hand, I found
> it does for my alanine-in-12 A water box system when I rerun the trajectory.
> Here is my sander input:
> # md_rerun.in
> &cntrl
> imin=5,
> ntx=5,
> maxcyc=1,
> irest=0,
> temp0=300.0,
> ioutfm=0,
> ntwf=1,
> ntwx=1,
> cut=10.0,
> ntb=1,
> /
>
> and in the output for cut=10:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -7.5647E+03 1.4040E+01 1.0199E+02 O 2168
>
> BOND = 1.6571 ANGLE = 8.7221 DIHED =
> 12.0941
> VDWAALS = 1079.3543 EEL = -8714.0624 HBOND =
> 0.0000
> 1-4 VDW = 3.0208 1-4 EEL = 44.5127 RESTRAINT =
> 0.0000
> minimization completed, ENE= -.75647012E+04 RMS= 0.140397E+02
>
> changing the cut=10 to cut=8 gives:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -7.4416E+03 1.3970E+01 9.7058E+01 O 2168
>
> BOND = 1.6571 ANGLE = 8.7221 DIHED =
> 12.0941
> VDWAALS = 1097.0112 EEL = -8608.5697 HBOND =
> 0.0000
> 1-4 VDW = 3.0208 1-4 EEL = 44.5127 RESTRAINT =
> 0.0000
> minimization completed, ENE= -.74415517E+04 RMS= 0.139702E+02
>
> As you can see, the EEL part changes from -8714.0624 to -8608.5697
> kcal/mol, which is definitely not neglectable.
> I wonder if any experts know what could be the probable reason.
>
> Best regards,
> Ge
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 06/OG07
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4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Tue Aug 20 2024 - 08:30:02 PDT
