Thank you very much guys! I will search for some reading. If you can suggest a tutorial I will appreciate.<br><br>
<div class="gmail_quote">On Thu, Jan 19, 2012 at 11:57 AM, René Pool <span dir="ltr"><<a href="mailto:r.pool@vu.nl">r.pool@vu.nl</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Hi,<br><br>If I understand the question correctly, you want to know the water chemical potential in the water/protein/ligand system.<br>
If so, in principle it should be possible to approximate the water chemical potential using test particle insertion. Gromacs has a utility for that.<br><br>Cheers,<br>René<br><br>==============================<u></u>=======================<br>
René Pool<br><br>Division of Molecular and Computational Toxicology<br>Department of Chemistry and Pharmaceutical Sciences<br>Vrije Universiteit Amsterdam<br>De Boelelaan 1083<br>1081HV AMSTERDAM, the Netherlands<br>-----<br>
IBIVU/Bioinformatics<br>Department of Computer Science<br>Vrije Universiteit Amsterdam<br>De Boelelaan 1081a<br>1081HV AMSTERDAM, the Netherlands<br><br>Room P 2.75<br>E: <a href="mailto:r.pool@vu.nl" target="_blank">r.pool@vu.nl</a><br>
T: <a href="tel:%2B31%2020%20598%2076%2012" target="_blank" value="+31205987612">+31 20 598 76 12</a><br>F: <a href="tel:%2B31%2020%20598%2076%2010" target="_blank" value="+31205987610">+31 20 598 76 10</a><br>==============================<u></u>=======================
<div class="im HOEnZb"><br><br><br>On 01/19/2012 02:49 PM, Ivan Gladich wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">On 01/19/2012 11:34 AM, Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Does anyone can help?<br>Dear Gmx Users,<br>I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system?<br>
Please, advise me to do some further reading, suggest method, maybe tutorial?<br>Thank you,<br>Steven<br></blockquote>Dear Steven<br>I am not an expert of protein - ligand system...<br>However the chemical potential of a i-th specie is the derivative of the potential energy in function of the number of the i-particles present in the system.<br>
As far as I know (and if I am not wrong), in GROMACS the number of particle is fixed along all the simulation, i.e., you cannot change the number of particles during the simulation.<br>Therefore, you cannot simply obtain the chemical potential from one single run...<br>
I suggest you to search in literature; maybe you can combine different runs to obtain the chemical potential...but I do not want to say you something wrong since I do not have experience in such systems.<br><br>Good luck<br>
Ivan<br><br></blockquote>-- <br></div>
<div class="HOEnZb">
<div class="h5">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br></div></div></blockquote></div><br>