content of amber output:mden

From: Thomas C. Bishop <>
Date: Fri 21 Jan 2000 11:01:55 -0600

Dear amber,

While most of the output to the "mden" file containing the extensive
energy data from a simulation is self-explainitory some items are not
so clear, and manuals 1 and 2 provide no information.

Information regarding how the data on lines L9 and L5/6 is calculated
would be greatly appreciated. In particular how does the
"configuration" of the system
(box size, solute/solven pointers, etc...) affect the calculation of the
virial terms and what are the AV_* terms?

FYI: A search thru manual1.pdf and manual2.pdf for the keyword "moment"
does not provide information regarding the AV_* data and the word
"virial" only appears once in manual1 in relation to gibbs and not at
all in manual2.


L0 Nsteps time(ps) Etot EKinetic
L1 Temp T_solute T_solv Pres_scal_solu
L2 Pres_scal_solv BoxX BoxY BoxZ
L3 volume pres_X pres_Y pres_Z
L4 Pressure EKCoM_x EKCoM_y EKCoM_z
L6 VIRIAL_tot E_pot E_vdw E_el
L7 E_hbon E_bon E_angle E_dih
L8 E_14vdw E_14el E_const E_pol
L9 AV_permMoment AV_indMoment AV_totMoment Density

Center for Bioenvironmental Research
Tulane University Office
Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
1430 Tulane Avenue
New Orleans, LA 70112
Phone: 504-988-6203   Fax: 504-585-6428
Xavier University Office
Division of Basic Pharmaceutical Sciences
College of Pharmacy
7325 Palmetto Street
New Orleans, LA 70125
Phone: 504-485-5106   Fax: 504-485-7930
Received on Fri Jan 21 2000 - 09:01:55 PST
Custom Search