<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>Hello,</DIV>
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<DIV>I have calculated the cumulative number from -cn for the usnic acid solvated by methanol molecules, but this result is enough different to those obtained by integration of the 4*pi*(number density)*area(gr. r2dr) until the first minimum of the RDF. I would like to know how the cumulative number is calculate.</DIV>
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<DIV>Thanks,</DIV>
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<DIV>Juliana Angeiras Batista da Silva</DIV>
<DIV>Laboratório de Química Teórica e Computacional</DIV>
<DIV>Departamento de Química Fundamental</DIV>
<DIV>Universidade Federal de Pernambuco.<BR></DIV>
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<B><SPAN style="FONT-WEIGHT: bold">De:</SPAN></B> "chris.neale@utoronto.ca" <chris.neale@utoronto.ca><BR><B><SPAN style="FONT-WEIGHT: bold">Para:</SPAN></B> gmx-users@gromacs.org<BR><B><SPAN style="FONT-WEIGHT: bold">Enviadas:</SPAN></B> Quarta-feira, 4 de Maio de 2011 14:01:26<BR><B><SPAN style="FONT-WEIGHT: bold">Assunto:</SPAN></B> [gmx-users] free energy<BR></FONT><BR>Dear Gavin:<BR><BR>I'm not seeing a lot of effort on your part to answer these questions. <BR>I suspect that you can answer some of this. Good luck!<BR><BR>Chris.<BR><BR>-- original message --<BR><BR>The current simulations are currently in vacuum. Does the following mdp<BR>file seem ok. Note that this is a production run using the final<BR>configuration after a lengthy equilibration. Also I was thinking about<BR>trying to prevent the other chains from entering the specific site; is<BR>there a a way to implement this in gromacs.<BR><BR>Gavin<BR><BR>chris.neale at utoronto.ca
wrote:<BR>> yes it will, and so will it affect the profile if water molecules or<BR>> ions go in when both chains are absent.<BR>><BR>> You'll need to determine what question you are trying to answer and<BR>> also think pretty hard about what your PMF really means in the context<BR>> of this system.<BR>><BR>> Chris.<BR>><BR>> -- original message --<BR>><BR>><BR>> Hi Chris<BR>><BR>> My windows are restrained obviously using the force constant in the mdp<BR>> file. The trajectories that I have viewed are those of the individual<BR>> biased sampling windows. I have not put on the unbiased simulations yet.<BR>> There is also the following issue: The simulations involve two identical<BR>> molecules containing hydrocarbon chains. I calculate the PMF to take a<BR>> specific hydrocarbon chain of one molecule out of a specific site on the<BR>> neighbouring molecule. When this guest chain goes out,
other chains can<BR>> go in (intramolecular or intermolecular). Will this affect the profile?<BR>><BR>> Gavin<BR><BR><BR>--<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists"
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