<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Hello all</DIV>
<DIV>I had simulated Tip4p-2005 water system with different concentrations of MgCl2 and Cacl2 salts. I have calculated the Surface tensions of the systems and I see that presence of the salt increases the S.T of water layer.</DIV>
<DIV>Now to do more analysis i want to calculate the contributions of water and ions to the electrostatic potential .</DIV>
<DIV>I should use g_potential command.</DIV>
<DIV> </DIV>
<DIV>I need an index file. Do I need to specify water, Mg and Cl groups in the index file?</DIV>
<DIV>is this command format corect?</DIV>
<DIV> </DIV>
<DIV>g_potential -f traj.trr -n index.ndx -s topol.tpr ?</DIV>
<DIV> </DIV>
<DIV>Please let me know if I should consider anything else?</DIV>
<DIV>thanks</DIV>
<DIV>Regards</DIV>
<DIV>D.Aghaie<BR><BR>--- On <B>Fri, 5/13/11, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] pressure in NPT and NVT<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Friday, May 13, 2011, 5:36 PM<BR><BR>
<DIV class=plainMail><BR><BR>Nilesh Dhumal wrote:<BR>> Hello,<BR>> <BR>> I am using NPT simulation for water - spce model (opls-aa force field).<BR>> I have the reference pressure set at ref_p = 1.0 bar.<BR>> I checked the average pressure using g_energy and it is 2.81972 bar.<BR>> <BR>> Why there increase in pressure?<BR>> <BR>> <BR><BR>Probably the system is not yet equilibrated.<BR><BR>> <BR>> For NVT simulatin I get the value around average pressure 710.685 bar.<BR>> <BR>> I am running the simulation at 295 k and average temp. is 294.98 K which<BR>> look ok.<BR>> <BR>> <BR>> Can you tell why there is increase in pressure for NPT and why there is<BR>> so high value of pressure in NVT.<BR>> <BR><BR>Because the box is fixed. It cannot respond to internal forces in your system. Pressure values during NVT don't mean much.<BR><BR>-Justin<BR><BR>> I am using gromacs version
4.0.7.<BR>> <BR>> Thanks<BR>> <BR>> Nilesh<BR>> <BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=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"
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