________________________________
Hi All,
like Amber tutorial A7, I tried to carry out REMD simulation in Amber 11 (as it's specified, tutorial should also work with this version). In '' mdout '' files I noticed that '' EPtot '' values for the last step of MD before swapping were different from '' myEptot '' ones used to calculate the exchange probability and it looks inconsistent.
So I made at once Amber tests to check software compilation for accuracy and they have been passed; furthermore the same tutorial was tried in Amber 10 and no mismatches between these values were found.
Can I use Amber 11 to simulate my system anyway or do you think Amber 10 would work better?
Fragments of the 2 '' mdout '' files for the first replica are wrote out below as you can check '' EPtot '' and '' myEptot '' values on your own:
Amber 10 results:
===============================================================================
NSTEP = 500 TIME(PS) = 203.000 TEMP(K) = 293.90 PRESS = 0.0
Etot = 83.0526 EKtot = 79.4283 EPtot = 3.6242
BOND = 22.4261 ANGLE = 38.9603 DIHED = 86.4959
1-4 NB = 22.7479 1-4 EEL = 632.8255 VDWAALS = -25.9882
EELEC = -707.9128 EGB = -66.2172 RESTRAINT = 0.2868
EAMBER (non-restraint) = 3.3375
TEMP0 = 269.5000 REPNUM = 1 EXCHANGE# = 3
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.287
===============================================================================
REMD: myEptot= 3.6242 myTargetTemp= 269.50 mytemp= 293.90
==========================REMD EXCHANGE CALCULATION==========================
Exch= 4 RREMD= 0
Replica Temp= 269.50 Indx= 1 Rep#= 1 EPot= 3.62
Partner Temp= 300.00 Indx= 2 Rep#= 2 EPot= 21.91
Not controlling exchange.
Rand= 0.456420E+00 MyScaling= -1.00 Success= F
========================END REMD EXCHANGE CALCULATION========================
Amber 11 results:
===============================================================================
NSTEP = 500 TIME(PS) = 203.000 TEMP(K) = 238.75 PRESS = .0
Etot = 72.6662 EKtot = 64.5229 EPtot = 8.1433
BOND = 18.1102 ANGLE = 47.0878 DIHED = 83.7739
1-4 NB = 23.3925 1-4 EEL = 638.6269 VDWAALS = -25.4731
EELEC = -704.7544 EGB = -72.6212 RESTRAINT = .0008
EAMBER (non-restraint) = 8.1425
TEMP0 = 269.5000 REPNUM = 1 EXCHANGE# = 3
------------------------------------------------------------------------------
NMR restraints: Bond = .000 Angle = .000 Torsion = .001
===============================================================================
REMD: myEptot= 8.5716 myTargetTemp= 269.50 mytemp= 238.75
==========================REMD EXCHANGE CALCULATION==========================
Exch= 4 RREMD= 0
Replica Temp= 269.50 Indx= 1 Rep#= 1 EPot= 8.57
Partner Temp= 300.00 Indx= 2 Rep#= 2 EPot= 20.02
Not controlling exchange.
Rand= .336937E-01 MyScaling= -1.00 Success= F
========================END REMD EXCHANGE CALCULATION========================
Thank you in advance.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 25 2011 - 03:30:03 PDT
