Dear all,
A follow-up message for the question on the periodic bondary condition.
The command I used is
$sander -O -i nef.in -p nef.top -c nef.xyz -o $output
The input file 'nef.in' for sander is like
======================================
ntt = 0
temp0 = 29.90, tempi= 29.90,
dt = 0.0001, nstlim = 11,
ntwx = 1, ntwv = 1, ntwe = 1, ntb = 1,
ntpr = 1, cut = 6.11,
ntx = 1, irest = 0
=======================================
I used tleap to construct "nef.top" and "nef.xyz"
-----------------------------------------------------------------------
nef = loadpdb nef.pdb
set nef box 14.2223
saveamberparm nef nef.top nef.xyz
----------------------------------------------------------------------
nef.xyz is based on a typical FCC(face center cubic) structure of 108 atoms
I checked the force first. I noticed that the forces are very different if a
displacement of every particle in the box was put in the file nef.xyz, i.e,
(x-a, y-a, z-a), where a is the displacement for each particle, i.e. a
translational move of the initial box. However, if the PBC is applied, the
displacement a will not affect the force at all.
For example, the first file "nef.xyz"
108
7.1111500 7.1111500 7.1111500 9.4811500 9.4811500 7.1111500
7.1111500 9.4811500 9.4811500 9.4811500 7.1111500 9.4811500
11.8521500 7.1111500 7.1111500 14.2221500 9.4811500 7.1111500
11.8521500 9.4811500 9.4811500 14.2221500 7.1111500 9.4811500
16.5931500 7.1111500 7.1111500 18.9631500 9.4811500 7.1111500
16.5931500 9.4811500 9.4811500 18.9631500 7.1111500 9.4811500
7.1111500 11.8521500 7.1111500 9.4811500 14.2221500 7.1111500
7.1111500 14.2221500 9.4811500 9.4811500 11.8521500 9.4811500
11.8521500 11.8521500 7.1111500 14.2221500 14.2221500 7.1111500
11.8521500 14.2221500 9.4811500 14.2221500 11.8521500 9.4811500
16.5931500 11.8521500 7.1111500 18.9631500 14.2221500 7.1111500
16.5931500 14.2221500 9.4811500 18.9631500 11.8521500 9.4811500
7.1111500 16.5931500 7.1111500 9.4811500 18.9631500 7.1111500
7.1111500 18.9631500 9.4811500 9.4811500 16.5931500 9.4811500
11.8521500 16.5931500 7.1111500 14.2221500 18.9631500 7.1111500
11.8521500 18.9631500 9.4811500 14.2221500 16.5931500 9.4811500
16.5931500 16.5931500 7.1111500 18.9631500 18.9631500 7.1111500
16.5931500 18.9631500 9.4811500 18.9631500 16.5931500 9.4811500
7.1111500 7.1111500 11.8521500 9.4811500 9.4811500 11.8521500
7.1111500 9.4811500 14.2221500 9.4811500 7.1111500 14.2221500
11.8521500 7.1111500 11.8521500 14.2221500 9.4811500 11.8521500
11.8521500 9.4811500 14.2221500 14.2221500 7.1111500 14.2221500
16.5931500 7.1111500 11.8521500 18.9631500 9.4811500 11.8521500
16.5931500 9.4811500 14.2221500 18.9631500 7.1111500 14.2221500
7.1111500 11.8521500 11.8521500 9.4811500 14.2221500 11.8521500
7.1111500 14.2221500 14.2221500 9.4811500 11.8521500 14.2221500
11.8521500 11.8521500 11.8521500 14.2221500 14.2221500 11.8521500
11.8521500 14.2221500 14.2221500 14.2221500 11.8521500 14.2221500
16.5931500 11.8521500 11.8521500 18.9631500 14.2221500 11.8521500
16.5931500 14.2221500 14.2221500 18.9631500 11.8521500 14.2221500
7.1111500 16.5931500 11.8521500 9.4811500 18.9631500 11.8521500
7.1111500 18.9631500 14.2221500 9.4811500 16.5931500 14.2221500
11.8521500 16.5931500 11.8521500 14.2221500 18.9631500 11.8521500
11.8521500 18.9631500 14.2221500 14.2221500 16.5931500 14.2221500
16.5931500 16.5931500 11.8521500 18.9631500 18.9631500 11.8521500
16.5931500 18.9631500 14.2221500 18.9631500 16.5931500 14.2221500
7.1111500 7.1111500 16.5931500 9.4811500 9.4811500 16.5931500
7.1111500 9.4811500 18.9631500 9.4811500 7.1111500 18.9631500
11.8521500 7.1111500 16.5931500 14.2221500 9.4811500 16.5931500
11.8521500 9.4811500 18.9631500 14.2221500 7.1111500 18.9631500
16.5931500 7.1111500 16.5931500 18.9631500 9.4811500 16.5931500
16.5931500 9.4811500 18.9631500 18.9631500 7.1111500 18.9631500
7.1111500 11.8521500 16.5931500 9.4811500 14.2221500 16.5931500
7.1111500 14.2221500 18.9631500 9.4811500 11.8521500 18.9631500
11.8521500 11.8521500 16.5931500 14.2221500 14.2221500 16.5931500
11.8521500 14.2221500 18.9631500 14.2221500 11.8521500 18.9631500
16.5931500 11.8521500 16.5931500 18.9631500 14.2221500 16.5931500
16.5931500 14.2221500 18.9631500 18.9631500 11.8521500 18.9631500
7.1111500 16.5931500 16.5931500 9.4811500 18.9631500 16.5931500
7.1111500 18.9631500 18.9631500 9.4811500 16.5931500 18.9631500
11.8521500 16.5931500 16.5931500 14.2221500 18.9631500 16.5931500
11.8521500 18.9631500 18.9631500 14.2221500 16.5931500 18.9631500
Then the force is
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
4.264024899510500E-002 0.000000000000000E+000 5.522798184521141E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
2.597452412639459E-003 3.663250348465068E-002 0.134501041258013
2.976381915174679E-005 0.000000000000000E+000 9.786853777336257E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
-4.261048517595324E-002 0.000000000000000E+000 5.521620223353677E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 1.260541012453736E-002 8.528080492325615E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
3.729752070572476E-002 5.528691680310158E-002 0.178450536781642
-9.180185730501808E-002 5.778507560138039E-002 0.134489985488216
-1.315187272174487E-003 4.524437486800894E-002 -4.393474825249220E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 3.005588155903929E-002 5.521976416664848E-002
9.184870571818743E-002 3.996696789401211E-002 0.134501041258013
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
1.514451967322923E-002 -0.121836696175586 0.134489985488216
4.271127049771597E-002 3.729752070572475E-002 0.178450536781642
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
4.262317919052712E-002 0.000000000000000E+000 -4.262317919052712E-002
-1.526273337669177E-002 -0.147000075331078 0.134489985488216
-0.134412342480971 -1.526273337669177E-002 0.134489985488216
0.000000000000000E+000 -8.525108884474261E-002 1.254569522611357E-002
0.130560972077048 8.790863653722229E-002 6.042275256132802E-002
0.000000000000000E+000 9.786853777336257E-002 1.260541012453736E-002
8.528080492325615E-002 0.000000000000000E+000 2.976381915174506E-005
1.251585095787790E-002 0.000000000000000E+000 1.251585095787790E-002
-3.862339568797764E-002 0.131856679960927 0.105674107166796
1.774145586756929E-002 0.175822728455908 5.343207116267528E-003
5.979534750771148E-005 0.000000000000000E+000 -1.251585095787789E-002
-1.263544165289332E-002 0.000000000000000E+000 1.251585095787790E-002
-9.179141572662942E-002 0.131861886616876 6.041317447272065E-002
-1.660514046649756E-002 0.177136995720328 1.529087320207821E-002
-8.390683972855204E-002 -1.314169847196402E-003 -9.917053309891254E-003
0.000000000000000E+000 5.516818649770370E-002 5.516818649770370E-002
0.133170221022241 4.402498345287152E-002 0.104348786493807
0.000000000000000E+000 5.979534750771148E-005 5.979534750771148E-005
0.177136269517223 1.642791480625483E-002 1.529232530200243E-002
2.037190114303933E-002 -1.834036521582133E-002 0.152215653900981
4.405556963586117E-002 4.668137155240697E-002 0.110878273584300
2.296918131674231E-002 2.746711062023385E-003 1.795161859752892E-002
1.194570455533700E-004 2.296845511363747E-002 1.795016649760470E-002
2.207384484328326E-002 6.430728802820854E-002 0.109587603787609
-0.177019911216010 5.345389441550844E-003 2.168808487103728E-002
-2.189151569297228E-002 1.432271712082239E-003 2.746538976501553E-003
-0.177018265069560 1.905853289597800E-002 2.716946514140312E-003
0.000000000000000E+000 -9.786853777336257E-002 1.254588248623385E-002
0.133176444426902 -0.131785814361321 1.645806073454367E-002
-1.314169847196402E-003 7.398961238655341E-002 2.658512546410426E-003
0.177136995720328 -1.660514046649755E-002 2.715226896692603E-003
2.296849354969717E-002 2.470037296293398E-002 6.824880930909788E-002
8.812143969516746E-005 -0.178332170891123 2.037309070600384E-002
1.643021624818965E-002 -0.177018316593505 2.716510843933817E-003
1.432271712082232E-003 -2.189151569297224E-002 2.746538976501581E-003
-1.926640173515231E-002 -1.926640173515229E-002 2.559574756616718E-002
-0.133086289221396 -0.137030645559676 1.646099015436769E-002
-1.792185404964589E-002 -0.178331978024715 8.896629456542349E-005
-0.177017590256200 -1.660763263827136E-002 2.717963641116733E-003
0.000000000000000E+000 -4.263152786442490E-002 -5.521976416664848E-002
0.134501041258013 0.134501041258013 -1.526101395119929E-002
0.000000000000000E+000 5.521620223353677E-002 -5.519821802605965E-002
1.314049383369009E-003 -1.313661431210276E-003 -1.520319085475400E-002
1.254588248623385E-002 0.000000000000000E+000 -9.786853777336257E-002
8.869877704190579E-005 0.178450536781642 -1.791868152781204E-002
1.514434751100009E-002 0.131860142967551 -0.139670141932980
0. -1.260541012453736E-002 0.000000000000000E+000 -9.786853777336257E-002
-0.134412342480971 0.134489985488216 -1.526273337669176E-002
-1.394817556666596E-002 0.133175427678191 -0.149628248417061
4.525253630989801E-002 -4.656755712374162E-002 -1.313374194963909E-003
0.000000000000000E+000 1.251585095787790E-002 -1.263544165289332E-002
0.178450536781642 8.869877704191509E-005 -1.791868152781201E-002
0.000000000000000E+000 -1.254561477702965E-002 -8.522100957574844E-002
0.133174700777577 1.382978970097428E-002 -0.149629701697103
2.296866544353827E-002 2.296866544353829E-002 -2.320647091611741E-002
1.185587569266719E-004 1.185587569266719E-004 -2.320578295739159E-002
1.774409327737428E-002 2.719153331644630E-003 -0.196180417884048
8.986554936386143E-005 1.774336637676022E-002 -0.196178964604006
-2.320647091611745E-002 2.296866544353828E-002 -2.320647091611741E-002
-0.178331978024715 8.896629456542349E-005 -1.792185404964586E-002
-1.660656933900602E-002 1.403696266820381E-003 -0.180961604390741
-0.133086289221396 1.646099015436769E-002 -0.137030645559676
0.000000000000000E+000 -9.786853777336257E-002 -1.260541012453736E-002
0.134489985488216 -0.134412342480971 -1.526273337669178E-002
-8.787491599676585E-002 8.960844358163597E-006 6.740953505176953E-002
0.133175427678191 -1.394817556666596E-002 -0.137040515566954
2.296866544353828E-002 -2.320647091611747E-002 -2.320647091611738E-002
8.896629456542002E-005 -0.178331978024715 -1.792185404964589E-002
1.514570544372783E-002 -0.134401019193651 -0.134401019193651
1.403696266820371E-003 -1.660656933900601E-002 -0.180961604390741
-2.320647091611745E-002 -2.320647091611745E-002 -2.320647091611738E-002
-0.134401019193651 -0.134401019193651 -1.526445379832693E-002
-1.526445379832692E-002 -0.134401019193651 -0.134401019193651
-0.134401019193651 -1.526445379832692E-002 -0.134401019193651
000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
However, if all coordinates of the particle in "nef.xyz" are shifted by a
displacement ( - 14.222), the force are different.
For example, prepare a second file
"nef.xyz"
108
-7.1108500 -7.1108500 -7.1108500 -4.7408500 -4.7408500 -7.1108500
-7.1108500 -4.7408500 -4.7408500 -4.7408500 -7.1108500 -4.7408500
-2.3698500 -7.1108500 -7.1108500 0.0001500 -4.7408500 -7.1108500
-2.3698500 -4.7408500 -4.7408500 0.0001500 -7.1108500 -4.7408500
2.3711500 -7.1108500 -7.1108500 4.7411500 -4.7408500 -7.1108500
2.3711500 -4.7408500 -4.7408500 4.7411500 -7.1108500 -4.7408500
-7.1108500 -2.3698500 -7.1108500 -4.7408500 0.0001500 -7.1108500
-7.1108500 0.0001500 -4.7408500 -4.7408500 -2.3698500 -4.7408500
-2.3698500 -2.3698500 -7.1108500 0.0001500 0.0001500 -7.1108500
-2.3698500 0.0001500 -4.7408500 0.0001500 -2.3698500 -4.7408500
2.3711500 -2.3698500 -7.1108500 4.7411500 0.0001500 -7.1108500
2.3711500 0.0001500 -4.7408500 4.7411500 -2.3698500 -4.7408500
-7.1108500 2.3711500 -7.1108500 -4.7408500 4.7411500 -7.1108500
-7.1108500 4.7411500 -4.7408500 -4.7408500 2.3711500 -4.7408500
-2.3698500 2.3711500 -7.1108500 0.0001500 4.7411500 -7.1108500
-2.3698500 4.7411500 -4.7408500 0.0001500 2.3711500 -4.7408500
2.3711500 2.3711500 -7.1108500 4.7411500 4.7411500 -7.1108500
2.3711500 4.7411500 -4.7408500 4.7411500 2.3711500 -4.7408500
-7.1108500 -7.1108500 -2.3698500 -4.7408500 -4.7408500 -2.3698500
-7.1108500 -4.7408500 0.0001500 -4.7408500 -7.1108500 0.0001500
-2.3698500 -7.1108500 -2.3698500 0.0001500 -4.7408500 -2.3698500
-2.3698500 -4.7408500 0.0001500 0.0001500 -7.1108500 0.0001500
2.3711500 -7.1108500 -2.3698500 4.7411500 -4.7408500 -2.3698500
2.3711500 -4.7408500 0.0001500 4.7411500 -7.1108500 0.0001500
-7.1108500 -2.3698500 -2.3698500 -4.7408500 0.0001500 -2.3698500
-7.1108500 0.0001500 0.0001500 -4.7408500 -2.3698500 0.0001500
-2.3698500 -2.3698500 -2.3698500 0.0001500 0.0001500 -2.3698500
-2.3698500 0.0001500 0.0001500 0.0001500 -2.3698500 0.0001500
2.3711500 -2.3698500 -2.3698500 4.7411500 0.0001500 -2.3698500
2.3711500 0.0001500 0.0001500 4.7411500 -2.3698500 0.0001500
-7.1108500 2.3711500 -2.3698500 -4.7408500 4.7411500 -2.3698500
-7.1108500 4.7411500 0.0001500 -4.7408500 2.3711500 0.0001500
-2.3698500 2.3711500 -2.3698500 0.0001500 4.7411500 -2.3698500
-2.3698500 4.7411500 0.0001500 0.0001500 2.3711500 0.0001500
2.3711500 2.3711500 -2.3698500 4.7411500 4.7411500 -2.3698500
2.3711500 4.7411500 0.0001500 4.7411500 2.3711500 0.0001500
-7.1108500 -7.1108500 2.3711500 -4.7408500 -4.7408500 2.3711500
-7.1108500 -4.7408500 4.7411500 -4.7408500 -7.1108500 4.7411500
-2.3698500 -7.1108500 2.3711500 0.0001500 -4.7408500 2.37115
-2.3698500 -4.7408500 4.7411500 0.0001500 -7.1108500 4.7411500
2.3711500 -7.1108500 2.3711500 4.7411500 -4.7408500 2.3711500
2.3711500 -4.7408500 4.7411500 4.7411500 -7.1108500 4.7411500
-7.1108500 -2.3698500 2.3711500 -4.7408500 0.0001500 2.3711500
-7.1108500 0.0001500 4.7411500 -4.7408500 -2.3698500 4.7411500
-2.3698500 -2.3698500 2.3711500 0.0001500 0.0001500 2.3711500
-2.3698500 0.0001500 4.7411500 0.0001500 -2.3698500 4.7411500
2.3711500 -2.3698500 2.3711500 4.7411500 0.0001500 2.3711500
2.3711500 0.0001500 4.7411500 4.7411500 -2.3698500 4.7411500
-7.1108500 2.3711500 2.3711500 -4.7408500 4.7411500 2.3711500
-7.1108500 4.7411500 4.7411500 -4.7408500 2.3711500 4.7411500
-2.3698500 2.3711500 2.3711500 0.0001500 4.7411500 2.3711500
-2.3698500 4.7411500 4.7411500 0.0001500 2.3711500 4.7411500
2.3711500 2.3711500 2.3711500 4.7411500 4.7411500 2.3711500
2.3711500 4.7411500 4.7411500 4.7411500 2.3711500 4.7411500
14.2223000 14.2223000 14.2223000 90.0000000 90.0000000 90.000000000
and the force is
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
3.943727428683287E-003 -7.953174555033402E-007 3.942155777904609E-003
-7.529747735553743E-002 8.659537912072161E-002 1.313712955155562E-003
-4.265233553982573E-002 8.529289146797682E-002 -4.262257172067401E-002
5.390515273118551E-002 -3.474468101356645E-002 -3.942591655037865E-003
1.720855218074070E-007 1.783305984060231E-002 2.628152305096714E-003
-5.519821802605962E-002 4.266694507431134E-002 3.010740356294839E-006
-2.657744038726657E-003 0.129247714660547 -4.393628467582957E-002
-1.651806587490166E-002 1.651879257618296E-002 -1.720855218115269E-007
0.100426231525989 4.389171440179603E-002 6.699356202162868E-002
6.623813401143919E-003 -1.265750281414927E-003 -5.266528546649778E-003
1.783305984060230E-002 -2.598120776740778E-003 -8.523326820599106E-002
NaN NaN NaN
NaN NaN NaN
8.797341275852991E-002 4.138702057219931E-002 0.123892086065810
0.162141614476140 -4.910959777706507E-002 -9.048974490170629E-002
NaN NaN NaN
NaN NaN NaN
-4.786694744211915E-002 -4.129625713537587E-002 -1.315062581874851E-003
-0.266724065289845 -4.255078662327165E-002 -9.048884642139889E-002
NaN NaN NaN
NaN NaN NaN
NaN NaN NaN
0.190915357065759 -4.918109627440796E-002 -3.863696437690001E-002
NaN NaN NaN
NaN NaN NaN
NaN NaN NaN
NaN NaN NaN
NaN NaN NaN
-0.246252018364000 -2.679236932143350E-003 4.786834758309656E-002
-1.388986771676013E-002 -2.628997346551315E-003 -1.314387768515205E-003
-0.221437566105834 -1.304859974256604E-003 -8.918819769956010E-002
-1.520507962102738E-002 1.314439349941148E-003 -1.314439349941148E-003
1.313712955155564E-003 2.627980219574906E-003 -1.314267264419343E-003
4.922093924962956E-002 0.105763914256080 -4.659295903005467E-002
5.912641177998709E-002 -3.998271607406141E-002 -1.314439158260448E-003
2.985963451478330E-005 0.145685822485755 4.526836425388495E-002
1.718938411107013E-007 5.254508339225605E-003 -2.627808325733793E-003
4.790867839439824E-002 0.108391722581813 -5.053503462020780E-002
NaN NaN NaN
4.658207720904051E-002 5.913845910086595E-002 2.627808325733792E-003
1.718938411115686E-007 5.254508339225608E-003 -2.627808325733794E-003
2.628121562037566E-003 4.659520999763989E-002 -4.922241811879484E-002
-5.521603033969564E-002 -3.999476339494026E-002 -5.254508339225600E-003
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
8.917696878605214E-002 7.170568967614933E-002 -5.258732353365442E-002
4.219336377252192E-005 3.406057577294314E-002 -4.922457064872555E-002
1.388112951157594E-002 8.397023443947285E-002 -2.629433315641767E-003
0.147079876212523 5.310490186148644E-002 -2.646607594007529E-002
4.122540837929858E-002 7.297395990049771E-002 -0.101810613363516
-7.788372370138311E-002 -9.643720309246258E-002 -9.186059669747333E-002
NaN NaN NaN
-5.910859866188913E-002 6.436746529317264E-002 -1.520341638674035E-002
-5.345175626446336E-003 0.120853945156388 -8.795055923654473E-002
-5.912774437195806E-002 -4.392564409979643E-002 -2.628099057924621E-003
3.470966971606122E-002 -7.393839793973334E-002 -4.655110945396438E-002
-5.049463714404170E-002 7.301867623651929E-002 3.822237419695562E-007
2.628878699882297E-003 -2.646628657647181E-002 -1.314993965700623E-003
-4.262257172067401E-002 0.000000000000000E+000 -4.264055592815109E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
4.529723058887185E-002 -0.104466905608814 4.133537291134994E-002
2.556023036650715E-003 -7.179645308501870E-002 -4.135698901588919E-002
-8.917696878605219E-002 -4.655439706537811E-002 -4.001167722826884E-002
-5.286374382928351E-003 -0.150941228615640 4.789689878272362E-002
1.345407909479221E-003 5.351392638636052E-002 -1.797075429787846E-006
-3.983886538502991E-003 1.482924416411846E-002 -4.396643071872330E-002
-4.655439706537812E-002 -4.655439706537812E-002 2.628878699882298E-003
-3.972107118509076E-003 -0.148313248396066 4.921061173787918E-002
-4.654258724958148E-002 -0.119676276686115 4.527975389898742E-002
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
NaN NaN NaN
5.913094740628005E-002 5.918920004272905E-002 2.649052664355174E-003
5.653025161690571E-002 4.525011627004241E-002 1.313661431210276E-003
-1.344298792775221E-003 0.100436722645430 1.313712955155564E-003
NaN NaN NaN
NaN NaN NaN
-1.385983618840420E-002 8.786209346702056E-002 1.314387768515207E-003
1.720855218074070E-007 4.786793793501188E-002 4.523867670489191E-002
-2.615893674854113E-003 -1.313712955155560E-003 -1.314267264419340E-003
-2.687167868870591E-003 1.923962639364957E-002 3.962714095565451E-003
-1.305184830852009E-003 0.143043501615714 4.393394874883293E-002
0.105694359790114 2.043074494713659E-002 -2.627972476744734E-003
NaN NaN NaN
7.038936155993486E-002 -1.123156539366066E-002 -4.130891028946378E-002
NaN NaN NaN
4.521271617867728E-002 -2.356445980294886E-002 -8.923317048087667E-002
NaN NaN NaN
NaN NaN NaN
-1.285092495457264E-003 -0.106157168797600 -4.524937439905143E-002
-5.916787913233541E-002 -2.876225007617970E-002 -5.254890448362689E-003
-1.388045469821627E-002 0.178463976139159 1.284629677744613E-003
NaN NaN NaN
-8.916433149652614E-002 -3.404464382713052E-003 -2.628545985600935E-003
4.786996980123871E-002 -0.192344698979750 4.919452595012584E-002
0.000000000000000E+000 -1.257564630538561E-002 0.000000000000000E+000
1.314272992800467E-003 -7.887428008744403E-003 -1.314272992800467E-003
5.785680710624087E-002 -9.787003672247420E-002 -4.525060352167490E-002
1.242481975336249E-003 -7.968961263696621E-002 -4.264076625805201E-002
-4.129625713537587E-002 -5.781415092475571E-002 1.313712955155560E-003
1.720855218080575E-007 -3.040870614598789E-002 -2.628152305096710E-003
-6.173837247274760E-002 -0.189722683984491 -4.525065504562018E-002
-4.014495212524952E-003 -0.111070532169682 6.551499829494238E-003
-4.261052439979520E-002 -4.261052439979520E-002 0.000000000000000E+000
3.441135273244723E-007 -2.308960173652199E-002 -1.031053712260629E-007
-8.524514344134811E-002 -0.127921667784453 -4.262257172067405E-002
All the interactions between atoms are LJ-interactions. I have checked the
force between two atoms without PBC and it looked fine. Aparently something
is wrong when the PBC is applied.
Could anyone help me with that? Thank you very much!
Best regards
J. L.
On 9/18/07, Jun Liu <junliujun.gmail.com> wrote:
>
> Dear all,
>
> I have met a problem on using the periodic boundary coundition.
>
> I prepared a file (nef.pdb) which contains the coordinates (x,y,z) of a
> FCC(face center cubic) structure. The interaction between particles are the
> LJ-potential.
>
> nef = loadpdb nef.pdb
> set nef box 14.2223
> saveamberparm nef nef.top nef.xyz
>
> Then I set "ntb = 1" and "cut = 6.11". Before I run the MD simulation, I
> checked the force first. I noticed that the forces are very different if a
> displacement of every particle in the box was put in the file nef.pdb, i.e,
> (x-a, y-a, z-a), where a is the displacement for each particle, i.e. a
> translational move of the initial box. However, if the PBC is applied, the
> displacement a will not affect the force at all. Does anyone have a clue on
> what wrong with what I did?
>
> Thank you very much!
>
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Received on Sun Sep 23 2007 - 06:07:15 PDT
