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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Dear Gromacs users,</SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman"
size=3> </FONT><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I seem to be having trouble with
trjconv. I have run a short simulation and want to write out a trajectory
with positions and forces.<SPAN style="mso-spacerun: yes"> </SPAN>However,
when using trjconv to write out the trajectory I get the same result whether I
try and write out velocities or forces:</SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"> </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">> mpirun -np 2 mdrun -np
2 -v -deffnm pr1<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">> trjconv -f pr1.trr -s
pr1.tpr -force -b 30 -e 40 -o test1.gro</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">> trjconv -f pr1.trr -s
pr1.tpr -vel -b 30 -e 40 -o test2.gro</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">> head -5
test1.gro</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Generated by trjconv :
Protein in water t=<SPAN style="mso-spacerun: yes">
</SPAN>30.00000</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">61767</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN>331SOL<SPAN
style="mso-spacerun: yes"> </SPAN>OW<SPAN
style="mso-spacerun: yes"> </SPAN>1<SPAN
style="mso-spacerun: yes"> </SPAN>0.745<SPAN
style="mso-spacerun: yes"> </SPAN>1.223<SPAN
style="mso-spacerun: yes"> </SPAN>1.235 -0.8542<SPAN
style="mso-spacerun: yes"> </SPAN>0.4057 -0.0772</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN>331SOL<SPAN
style="mso-spacerun: yes"> </SPAN>HW1<SPAN
style="mso-spacerun: yes"> </SPAN>2<SPAN
style="mso-spacerun: yes"> </SPAN>0.662<SPAN
style="mso-spacerun: yes"> </SPAN>1.257<SPAN
style="mso-spacerun: yes"> </SPAN>1.197 -0.0011<SPAN
style="mso-spacerun: yes"> </SPAN>2.1431 -1.5672</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN>331SOL<SPAN
style="mso-spacerun: yes"> </SPAN>HW2<SPAN
style="mso-spacerun: yes"> </SPAN>3<SPAN
style="mso-spacerun: yes"> </SPAN>0.803<SPAN
style="mso-spacerun: yes"> </SPAN>1.297<SPAN
style="mso-spacerun: yes"> </SPAN>1.208<SPAN
style="mso-spacerun: yes"> </SPAN>1.5836 -1.7723 -2.4831</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">> head -5
test2.gro</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Generated by trjconv :
Protein in water t=<SPAN style="mso-spacerun: yes">
</SPAN>30.00000</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">61767</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN>331SOL<SPAN
style="mso-spacerun: yes"> </SPAN>OW<SPAN
style="mso-spacerun: yes"> </SPAN>1<SPAN
style="mso-spacerun: yes"> </SPAN>0.745<SPAN
style="mso-spacerun: yes"> </SPAN>1.223<SPAN
style="mso-spacerun: yes"> </SPAN>1.235 -0.8542<SPAN
style="mso-spacerun: yes"> </SPAN>0.4057 -0.0772</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN>331SOL<SPAN
style="mso-spacerun: yes"> </SPAN>HW1<SPAN
style="mso-spacerun: yes"> </SPAN>2<SPAN
style="mso-spacerun: yes"> </SPAN>0.662<SPAN
style="mso-spacerun: yes"> </SPAN>1.257<SPAN
style="mso-spacerun: yes"> </SPAN>1.197 -0.0011<SPAN
style="mso-spacerun: yes"> </SPAN>2.1431 -1.5672</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><SPAN
style="mso-spacerun: yes"> </SPAN>331SOL<SPAN
style="mso-spacerun: yes"> </SPAN>HW2<SPAN
style="mso-spacerun: yes"> </SPAN>3<SPAN
style="mso-spacerun: yes"> </SPAN>0.803<SPAN
style="mso-spacerun: yes"> </SPAN>1.297<SPAN
style="mso-spacerun: yes"> </SPAN>1.208<SPAN
style="mso-spacerun: yes"> </SPAN>1.5836 -1.7723 -2.4831</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Here are the relevant lines
from my .mdp file:</SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; ** Options for Output
Control **</SPAN><SPAN style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">nstxout<SPAN
style="mso-tab-count: 3">
</SPAN>= 100 <o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">nstvout<SPAN
style="mso-tab-count: 3">
</SPAN>= 100 </SPAN><SPAN
style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">nstfout<SPAN
style="mso-tab-count: 3">
</SPAN>= 100</SPAN><SPAN
style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;<SPAN
style="mso-spacerun: yes"> </SPAN>Output freq for energies to
log and energy files</SPAN><SPAN
style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">nstlog<SPAN
style="mso-tab-count: 3">
</SPAN>= 100</SPAN><SPAN
style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">nstenergy<SPAN
style="mso-tab-count: 3">
</SPAN>= 100</SPAN><SPAN
style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;</SPAN><SPAN
style="FONT-FAMILY: 'Courier New'"><o:p></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: 'Courier New'"><FONT
size=3> <o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I get <SPAN
class=758335719-28092009>equivalent results </SPAN>whether I do all or part of
the trajectory and whether I write out the whole system or just one part.
As you can see from the .mdp file, I am using the same output frequencies for
everything.<SPAN style="mso-spacerun: yes"> </SPAN>I am running Gromacs
4.0.5</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"> </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Can anyone tell me what I'm doing
wrong? I apologize if it is a boneheaded error.</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"> </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Thank you in advance</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"> </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Guy Vigers</SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman"
size=3></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman"
size=3>(please ignore the boilerplate below:)</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></P></FONT></DIV></BODY></HTML>
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