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<DIV><FONT face=Arial>Hi,<BR><BR>I am a new user of GROMACS. I have sent this
message one week ago but did not get any answer. I am trying to run MD
simulation of one of the proteins. I followed the "getting started" tutorial. My
question is about minimization of my system in solvent. According to the
tutorial the minimization should be finished when either the minimization has
converged or a fixed number of steps has been performed. In my case the
minimization has converged before it reached the fixed number of steps. But the
potential energy after minimization IS NOT lower than potential energy
calculated by formula: -42(kJ/mole)xN (N is a number of SPC water molecules).
What is the problem? How can I fix it? The same problem I had for Ribonuclease
S-peptide given in tutorial. As I heard the problem might be a precision. Am I
correct? My calculations run in single precision, so I may need a double
precision. But I don't know how to change the precision. Can anyone help me
to change a single precission to double precision? Is there any other ways
to fix this problem? <BR><BR>My second question is about short and full MD
run. According to the tutorial to generate the input for the position restrained
mdrun we have the following command:<BR><BR>grompp -f pr -o pr -c after_em -r
after_em -p speptide<BR><BR>for full md to do the same thing we have the
following command:<BR><BR>grompp -v -f full -o full -c after_pr -p
speptide<BR><BR>We can see that full MD is quite similar to the restrained MD,
but there is a difference which makes impossible to run full MD without
restrained MD. In full MD we have "-c after_pr" which is an input file and
"after_pr" can be obtained from short MD run. Is it correct that we can't run
full MD run without short MD or is there any other way to run directly full MD
(for example, use the same files for full MD as used for short MD)?<BR><BR>I
look forward to hearing your reply,<BR><BR>With best wishes,<BR><BR>Gia
Maisuradze <BR></FONT></DIV></BODY></HTML>