[gmx-users] NVE of water

[Mark Abraham]

On 2/03/2010 12:39 AM, Ran Friedman wrote:
> Hi,
>
> I would still argue that double precision is important.

Oh? The discussion of Table 4 of 
http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC 
paper) suggested to me that single-precision NVE could be done well in 
GROMACS. Am I missing something?

Mark

> 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
>>>   >  ------------------------------------------------------
>>>   >
>>>   >  --
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>>
>