Dear Rahul,
I checked out your file and it seems to work fine for me.
Since the initial rmsd was the same as the target, I changed the
target to differ so I could get some restraint energy. As you can see
below, with target rmsd of 3.75 and current rmsd of 0.75, the energy
is 8578.8. when I solve E=1/2 k #atom (rmsd-target)^2 for #atoms = 1/2
* (2.0) * E/(3.75-0.75)^2 = 952.97 and the mask has 953 atoms. This
all works out.
try this and see if you get different results. (I also set ntpr=1 to
write info each step)
NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 5.77 PRESS = -1290.4
Etot = -62026.6397 EKtot = 271.0318 EPtot = -62297.6715
BOND = 374.0818 ANGLE = 973.3073 DIHED = 1259.6423
1-4 NB = 445.6128 1-4 EEL = 6043.9403 VDWAALS = 8903.7954
EELEC = -88876.8708 EHBOND = 0.0000 RESTRAINT = 8578.8194
EAMBER (non-restraint) = -70876.4909
EKCMT = 0.0000 VIRIAL = 6436.3440 VOLUME = 231019.5016
Density = 1.0131
Ewald error estimate: 0.4300E-04
Current RMSD from reference: 0.750
Current target RMSD: 3.750
On Fri, Apr 8, 2011 at 4:26 PM, Rahul Banerjee
<rahul.banerjee.chemistry.msu.edu> wrote:
> Dear Carlos,
>
> My input files are attached herewith. I have used the following comand to run TMD:
>
>> sander.MPI -O -i i2a_15.50_2-5.in -o i2a_15.50_2-5.out -p inactv_solv.prmtop -c rep1_i2a_15.50.rst.775 -r i2a_15.50_2-5.rst -x i2a_15.50_2-5.mdcrd -ref actv_trgt.inpcrd
>
> Please check the numbers in the file "i2a_15.50_2-5.out".
>
> Please let me know whether RESTRAINT potential can be calculated correctly from "Current RMSD from reference" and "Current target RMSD" for each iteration or not.
>
> With best regards,
> Rahul
>
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Received on Fri Apr 08 2011 - 14:00:04 PDT
