# [AMBER] Single Point Energy: sander x python sander

From: Alan <alanwilter.gmail.com>
Date: Thu, 13 Jan 2022 09:26:51 +0000

I'm trying to compare topologies in different platforms (mostly amber x
gromacs, using different convertors)

In my old times I used to use this:

cat << EOF >| mdin
Single point
&cntrl
imin=0, maxcyc=0,
ntmin=2,
ntb=0,
igb=0,
cut=999,
//
EOF

After reviewing Amber21 manual I updated to:
cat << EOF >| mdin
Single point
&cntrl
imin=0, maxcyc=0,
ntmin=2,
igb=6,
//
EOF

But when I compare my traditional way with the sander python module I can't
figure out why the energies differ.

Example:

cat << EOF >| tleap.in
source leaprc.protein.ff14SB
aaa14 = sequence {NALA ALA CALA}
SaveAmberParm aaa14 AAA14.prmtop AAA14.inpcrd
savepdb aaa14 aaa14.pdb
quit
EOF
tleap -f tleap.in

cat << EOF >| mdin
Single point
&cntrl
imin=0, maxcyc=0,
ntmin=2,
igb=6,
//
EOF

sander -O -i mdin -o mdout -p AAA14.prmtop -c AAA14r.inpcrd

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = 1.0270 EKtot = 0.0000 EPtot =
1.0270
BOND = 0.7730 ANGLE = 4.2777 DIHED =
14.9041
1-4 NB = 9.2288 1-4 EEL = 231.2899 VDWAALS =
3.8465
EELEC = -263.2930 EGB = 0.0000 RESTRAINT =
0.0000

# Now via python:
python3 <<EOF
import sander
# Using gas-phase calculations
inp = sander.gas_input()
with sander.setup('AAA14.prmtop', 'AAA14.inpcrd', box=None, mm_options=inp):
e, f = sander.energy_forces()
print(f"{inp.igb}, {inp.cut}, {inp.ntb}, {e.tot}, {e.elec}")
EOF
6, 1000.0, 0, 1.0036269011276318, -263.3224288217461

The only parameter that changed (AFAIK) was cutoff (9999 x 1000) but this
wouldn't affect the results.

So, I can't understand why Etot = 1.0270 <> 1.0036 (and everything else
differs as well). It's more than 2%!

This error difference in python is much bigger than the error I got when
using the same system and calculated the SPE using gromacs (but with
version 19.1, the last version capable of SPE in vacuum without pbc), after
converting the input files.
```--
Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
```
Received on Thu Jan 13 2022 - 01:30:02 PST
Custom Search