<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear Gromacs users</span></div><div><span>I have a question abut radius of gyration in proteins. I want to calculate it via MD simulation for calcium pump protein. Following the same method as described in justin lezozyme tutorial, we have dissolved the protein in water.</span></div><div><span>I want to know that is it wise to study this parameter for this protein out of membrane and only in the box of water???</span></div><div><span>Thanks</span></div><div><span>regards</span></div><div><span>D.M</span></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Anja Kuhnhold
<anja.kuhnhold@physik.uni-halle.de><br> <b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, 8 June 2012, 12:29<br> <b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Re: energy conservation: shift vs shifted user potential<br> </font> </div> <br>Hello all,<br><br>can someone give me a hint, please?<br>Do you need more information?<br>Has anyone had a similar problem.<br><br>I really need to figure that out, because I will simulate other systems<br>which can be run only with user tables.<br><br>Anja<br><br><br><br>-<br>> ----- Original Message -----<br>> ----- Original Message -----<br>> From Anja Kuhnhold <<a ymailto="mailto:anja.kuhnhold@physik.uni-halle.de" href="mailto:anja.kuhnhold@physik.uni-halle.de">anja.kuhnhold@physik.uni-halle.de</a>><br>> Date Wed, 06 Jun 2012 15:07:40 +0200<br>> To <a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject [gmx-users] energy conservation: shift vs shifted user potential<br>> Dear gmx-users,<br>> <br>> I have a problem concerning energy conservation when using user <br>> potentials (tables).<br>> I'm using gromacs 4.5.4<br>> I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 <br>> chains a 10 beads in a 26x26x26 periodic box).<br>> <br>> I tried different vdwtypes (cutoff always 3.24):<br>> The cut-off version does not conserve energy -- okay.<br>> The shift and switch versions conserve energy -- fine.<br>> <br>> Now I wanted to do the same with user tables:<br>> Simple Lennard-Jones table gives really the same results as the <br>> cut-off version -- good.<br>> <br>> But if I use a table with shifted Lennard-Jones potential it is not <br>> comparable to the shift
version<br>> and the energy is not conserved -- ?<br>> <br>> I use a shift function as written in the manual (chapter 4.1.5) -- <br>> there must be a factor alpha added in the constants A and B --<br>> (r1=0).<br>> <br>> The parameters are the same for shift version and shifted user version.<br>> <br>> Has someone an idea why the shifted user potential doesn't work in <br>> this way?<br>> <br>> Here is the mdp:<br>> <br>> <br>> integrator = md-vv<br>> dt = 0.0035<br>> nsteps = 1000<br>> nstxout = 1<br>> nstvout = 1<br>> nstfout
= 1<br>> nstlog = 1<br>> ns_type = grid<br>> pbc = xyz<br>> rvdw = 3.24<br>> rlist = 3.6<br>> tcoupl = no<br>> tc-grps = System<br>> tau_t = 2.0<br>> ref_t = 127.2717<br>> vdwtype
= user;Shift<br>> rcoulomb = 3.6;2.24;1.12<br>> coulombtype = Cut-off<br>> rvdw-switch = 0.0<br>> <br>> energygrps = bead<br>> energygrp_table = bead bead<br>> <br>> <br>> Thanks in advance<br>> Anja<br>> <br><br>--<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="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
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