[gmx-users] NVE of water

[Ran Friedman]

Hi,

I would still argue that double precision is important.
My comment on SHAKE was based on CHARMM - in Gromacs it indeed doesn't
matter for water.

Ran

Justin A. Lemkul wrote:
>
>
> Berk Hess wrote:
>> Hi,
>>
>> Shake is not relevant for water and also a time step of 2 fs should
>> be fine.
>> The cut-off's are the problem. You have a buffer size of 0.1 nm,
>> which is already smaller than 2 times the distance from the center of
>> geometry
>> of a water molecule to a hydrogen. You need some additional distance
>> for water diffusion. I would use a buffer of 0.25 to 0.3 nm.
>> You don't list you coulombtype setting. Use pme (or if you want
>> perfect energy
>> conservation: pme-switch), you can also use reaction-field-zero if
>> you really don't
>> want to use PME.
>> Then use nstlist=-1, run a short simulation and check in at the end
>> of your log file
>> that the neighbor list lifetime is somewhere between 5 and 20 steps.
>>
>> We should have a wiki entry for such details. Maybe there is one, but
>> I was too lazy
>> to check or make one.
>
> There was a basic NVE page; I have updated it based on your notes above:
>
> http://www.gromacs.org/Documentation/Terminology/NVE
>
> -Justin
>
>>
>> Berk
>>
>>  > Date: Mon, 1 Mar 2010 09:16:36 +0100
>>  > From: r.friedman at bioc.uzh.ch
>>  > To: gmx-users at gromacs.org
>>  > Subject: Re: [gmx-users] NVE of water
>>  >
>>  > Hi Andrea,
>>  > Did you use double precision? Also, I'd try a lower dt (say 1fs) and
>>  > shake tolerance (maybe 1E-8).
>>  > Good luck,
>>  > Ran
>>  >
>>  > Andrea wrote:
>>  > > Dear users,
>>  > >
>>  > > for test purposes in order to set up a bigger system, I try to
>> run NVE
>>  > > simulations of SPC water, but the energy increases very
>> rapidely. My
>>  > > guess is that the cutoffs I use are not good for water. I that the
>>  > > case ( I would be grateful for a good reference for suitable SPC
>> water
>>  > > parameters) or do I miss something else?
>>  > > My parameter file for the NVE is:
>>  > >
>>  > > title = NVE
>>  > > cpp = /lib/cpp
>>  > > integrator = md
>>  > > dt = 0.002 ; ps ! = 2 fs
>>  > > nsteps = 50000 ; total 100 ps
>>  > > nstxout = 5000
>>  > > nstvout = 5000
>>  > > nstxtcout = 0
>>  > > nstlog = 5000
>>  > > nstenergy = 5000
>>  > > nstlist = 10
>>  > > ns_type = grid
>>  > > rlist = 1.1
>>  > >
>>  > > unconstrained-start = yes
>>  > > constraints = all-bonds
>>  > > constraint_algorithm = shake
>>  > > shake_tol = 0.0001
>>  > > ;VdW
>>  > > vdwtype = Switch
>>  > > rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist
>>  > > rvdw_switch = 0.9
>>  > > gen_vel = no ; yes
>>  > > gen_temp = 300
>>  > > gen_seed = -1
>>  > > ;Temperature coupling
>>  > > tc_grps = system
>>  > > tcoupl = no ;nose-hoover
>>  > > tau_t = 0.1
>>  > > ref_t = 300
>>  > > ;Pressure coupling
>>  > > pcoupl = no
>>  > > optimize_fft = yes
>>  > >
>>  > > Any suggesions are really welcome.
>>  > >
>>  > > Thank you.
>>  > >
>>  > > Regards,
>>  > > Andrea Muntean
>>  >
>>  >
>>  > --
>>  > ------------------------------------------------------
>>  > Ran Friedman
>>  > Postdoctoral Fellow
>>  > Computational Structural Biology Group (A. Caflisch)
>>  > Department of Biochemistry
>>  > University of Zurich
>>  > Winterthurerstrasse 190
>>  > CH-8057 Zurich, Switzerland
>>  > Tel. +41-44-6355559
>>  > Email: r.friedman at bioc.uzh.ch
>>  > Skype: ran.friedman
>>  > ------------------------------------------------------
>>  >
>>  > --
>>  > gmx-users mailing list gmx-users at gromacs.org
>>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>  > Please search the archive at http://www.gromacs.org/search before
>> posting!
>>  > Please don't post (un)subscribe requests to the list. Use the
>>  > www interface or send it to gmx-users-request at gromacs.org.
>>  > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> ------------------------------------------------------------------------
>> New Windows 7: Find the right PC for you. Learn more.
>> <http://windows.microsoft.com/shop>
>>
>