From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Nov 11 2009 - 06:58:44 CST
Ha namd users,
can anybody tell me the formating of the output file, especially the
formatting of the following lines:
PRESSURE:
GPRESSURE:
PRESSAVG:
GPRESSAVG:
ENERGY:
Are the values in fixed columns or white space separated? Or is there any
criteria which can separate these values for 100%
I used the following python synthax to extract the values, but today it failed
for th first time because the formatting did no longer match:
def Energy(line) :
TS.append(int(line[7:16].strip()))
BOND.append(float(line[16:31].strip()))
ANGLE.append(float(line[31:46].strip()))
DIHED.append(float(line[46:61].strip()))
IMPRP.append(float(line[61:76].strip()))
ELECT.append(float(line[76:96].strip()))
VDW.append(float(line[96:112].strip()))
BOUNDARY.append(float(line[112:126].strip()))
MISC.append(float(line[126:141].strip()))
KINETIC.append(float(line[141:156].strip()))
TOTAL.append(float(line[156:176].strip()))
TEMP.append(float(line[176:191].strip()))
TOTAL2.append(float(line[191:206].strip()))
TOTAL3.append(float(line[206:221].strip()))
TEMPAVG.append(float(line[221:236].strip()))
# If "minimization on" was used these values are not populated
if not MINo :
PRESSURE.append(float(line[236:256].strip()))
GPRESSURE.append(float(line[256:271].strip()))
VOLUME.append(float(line[271:286].strip()))
PRESSAVG.append(float(line[286:301].strip()))
GPRESSAVG.append(float(line[301:316].strip()))
kind regards
Bjoern
-- Bjoern Olausson Martin-Luther-Universität Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
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