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Hi,<br><br>I have now added a check to grompp for the charge-group radii versus the buffer size<br>for the next Gromacs release.<br><br>Berk<br><br><hr id="stopSpelling">Date: Mon, 1 Mar 2010 09:33:13 +0100<br>Subject: Re: [gmx-users] NVE of water<br>From: andreamuntean@gmail.com<br>To: gmx-users@gromacs.org<br><br><div>Thank you for your hints. I'll give it a try right now.</div>
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<div>Regards,</div>
<div>Andrea<br><br></div>
<div class="ecxgmail_quote">2010/3/1 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span><br>
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<div>Hi,<br><br>Shake is not relevant for water and also a time step of 2 fs should be fine.<br>The cut-off's are the problem. You have a buffer size of 0.1 nm,<br>which is already smaller than 2 times the distance from the center of geometry<br>
of a water molecule to a hydrogen. You need some additional distance<br>for water diffusion. I would use a buffer of 0.25 to 0.3 nm.<br>You don't list you coulombtype setting. Use pme (or if you want perfect energy<br>
conservation: pme-switch), you can also use reaction-field-zero if you really don't<br>want to use PME.<br>Then use nstlist=-1, run a short simulation and check in at the end of your log file<br>that the neighbor list lifetime is somewhere between 5 and 20 steps.<br>
<br>We should have a wiki entry for such details. Maybe there is one, but I was too lazy<br>to check or make one.<br><br>Berk<br><br>> Date: Mon, 1 Mar 2010 09:16:36 +0100<br>> From: <a href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a><br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: Re: [gmx-users] NVE of water
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<div class="h5"><br>> <br>> Hi Andrea,<br>> Did you use double precision? Also, I'd try a lower dt (say 1fs) and<br>> shake tolerance (maybe 1E-8).<br>> Good luck,<br>> Ran<br>> <br>> Andrea wrote:<br>
> > Dear users,<br>> > <br>> > for test purposes in order to set up a bigger system, I try to run NVE<br>> > simulations of SPC water, but the energy increases very rapidely. My<br>> > guess is that the cutoffs I use are not good for water. I that the<br>
> > case ( I would be grateful for a good reference for suitable SPC water<br>> > parameters) or do I miss something else?<br>> > My parameter file for the NVE is:<br>> > <br>> > title = NVE<br>
> > cpp = /lib/cpp<br>> > integrator = md<br>> > dt = 0.002 ; ps ! = 2 fs<br>> > nsteps = 50000 ; total 100 ps<br>> > nstxout = 5000<br>> > nstvout = 5000<br>> > nstxtcout = 0<br>
> > nstlog = 5000<br>> > nstenergy = 5000<br>> > nstlist = 10<br>> > ns_type = grid<br>> > rlist = 1.1<br>> ><br>> > unconstrained-start = yes<br>> > constraints = all-bonds<br>
> > constraint_algorithm = shake<br>> > shake_tol = 0.0001<br>> > ;VdW<br>> > vdwtype = Switch<br>> > rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist<br>> > rvdw_switch = 0.9<br>> > gen_vel = no ; yes<br>
> > gen_temp = 300<br>> > gen_seed = -1<br>> > ;Temperature coupling<br>> > tc_grps = system<br>> > tcoupl = no ;nose-hoover<br>> > tau_t = 0.1<br>> > ref_t = 300<br>> > ;Pressure coupling<br>
> > pcoupl = no<br>> > optimize_fft = yes<br>> > <br>> > Any suggesions are really welcome.<br>> > <br>> > Thank you.<br>> > <br>> > Regards,<br>> > Andrea Muntean<br>
> <br>> <br>> -- <br>> ------------------------------------------------------<br>> Ran Friedman<br>> Postdoctoral Fellow<br>> Computational Structural Biology Group (A. Caflisch)<br>> Department of Biochemistry<br>
> University of Zurich<br>> Winterthurerstrasse 190<br>> CH-8057 Zurich, Switzerland<br>> Tel. +41-44-6355559<br>> Email: <a href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a><br>
> Skype: ran.friedman<br>> ------------------------------------------------------<br>> <br>> -- <br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>
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