[gmx-users] Pressure very high with chloroform and gromacs-4.5.5
Nuno Azoia
nazoia at gmail.com
Wed Oct 12 15:35:49 CEST 2011
I know that from the beginning. That's why I found very strange the
increasing on the system volume. My initial setup have a density of
~400g/L, and for liquid chloroform is ~1400g/L.
Using gromacs-4.5 I get densities of about 200 after 750ps simulation
time, and using 4.0 I get almost 500 after 1ns.
And I was using such low densities because I build the box using
genconf with the options -nbox and -dist, starting with one molecule
of chloroform. If I used small distance values I get LINCS warnings in
the energy minimization step. Using genbox to solvate one empty box
with chloroform, I get very strange behaviors, with a very large
amount of molecule overlap.
But as you said before, I now think that this should be also a
paralelization problem, not to mention the numerical instability
caused by this very low density.
And I think this is a paralelization problem associated with this
numerical instability judging from the system behavior.
In 4.5, using the option -nt in mdrun, I get some small droplets of
liquid chloroform, and in 4.0, using mpi, I get one large droplet of
chloroform. It looks like if 4.5 is treating the system like
independent small systems, while 4.0 is able to divide the system into
small, but interdependent systems.
On Wed, Oct 12, 2011 at 12:26 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 12/10/2011 8:04 PM, Nuno Azoia wrote:
>>
>> Thank you Mark for your answer!
>>
>> I agree with you when you say that the high pressure is not itself a
>> problem. To avoid that problem I change my system from 1000 molecules
>> to 27000 molecules, and the pressure change from several thousands to
>> several hundreds bar.
>> What I found very strange was the increasing volume (and pressure). My
>> system is very unstable, I know, because the density is very low, and
>> not the opposite, so I was expecting to see the box getting smaller.
>> Looking to the trajectory I can see a box almost empty (with empty I
>> mean empty space, with chloroform molecules aggregating in small
>> droplets), and that's why I found the system behavior very strange.
>
> Sounds like your initial density might be far too low. grompp reports it, so
> do check.
>
> Mark
>>
>> I will follow your suggestion concerning nsttcouple and nstpcouple and
>> the other initial conditions.
>>
>> Nuno Azoia
>>
>>
>> On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham<Mark.Abraham at anu.edu.au>
>> wrote:
>>>
>>> On 12/10/2011 2:22 AM, Nuno Azoia wrote:
>>>>
>>>> Hello!
>>>>
>>>> I found something very strange while making a CHCl3 box using
>>>> gromacs-4.5.5.
>>>> A look the mailing list, the manual and some release notes for
>>>> gromacs-4.5 and I couldn't found the answer for my problem. It's
>>>> possible that I'm doing something wrong, but I can not find what, so
>>>> I'm describe my problem.
>>>>
>>>> I start a chloroform box from scratch, using genconf, and I get o
>>>> chloroform box with 1000 molecules. I get energy minimization without
>>>> problems.
>>>> Then I've run some equilibration steps in a NVT ensemble and in the
>>>> end I get pressure in the order of hundreds of bar.
>>>
>>> The high pressure is not itself a problem - small numbers of molecules
>>> and
>>> short simulation times lead to doubtful statistics for pressure.
>>>
>>>> Then I change to
>>>> NPT conditions and both the pressure and the volume keep increasing
>>>> with time.
>>>
>>> Be sure to visualize your trajectory to confirm its behaviour matches
>>> what
>>> you expect from the trends in P and V.
>>>
>>>> To discard the possibility of a size problem, I repeat everything with
>>>> a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
>>>> was the same. Very high pressures (150-200 bar) and very low densities
>>>> (< 200 g/L) after 750 ps simulation time. And both volume and
>>>> pressure
>>>> increasing with time.
>>>>
>>>>
>>>> I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
>>>> getting very different (and better) results. After energy minimization
>>>> I run 50000 steps in a nvt ensemble and I got pressure around -30 bar
>>>> (Ok for me). After that I start to run the simulations in npt ensemble
>>>> and the pressure start to increase slowly, with negative values
>>>> because the system have very low densities (~400 g/L), and the volume
>>>> is decreasing. So I'm getting the normal reaction from the system.
>>>>
>>>>
>>>>
>>>> Where is the problem? There are some different parameters to set in
>>>> the mdp file and I didn't realize that, or is this a problem in
>>>> gromacs-4.5?
>>>
>>> It seems you are generating some numerical instability with your choice
>>> of
>>> initial and simulation conditions, and that gromacs-4.0 was luckier in
>>> avoiding the problem. If this is a parallel simulation, then the way
>>> communication is managed in order to organize T and P coupling changed
>>> going
>>> up to 4.5. For equilibration, I would encourage setting nsttcouple and
>>> nstpcouple to 1. Using a shorter time step can help with numerical
>>> instability. Berendsen T coupling or a larger coupling time constant
>>> might
>>> also help. After gentler NVT, then switch to NPT, let the box size
>>> stabilize, and finally move to larger coupling periods, time steps and
>>> v-rescale T coupling.
>>>
>>> Mark
>>>
>>>>
>>>> In both cases I used this parameters:
>>>>
>>>> -------------------------------------------------------------------------
>>>> integrator = md
>>>> dt = 0.002
>>>> nsteps = 50000
>>>> nstcomm = 1
>>>> nstxtcout = 500
>>>> xtc-precision = 1000
>>>> nstxout = 0
>>>> nstvout = 0
>>>> nstfout = 0
>>>> nstlog = 500
>>>> nstenergy = 500
>>>>
>>>> nstlist = 5
>>>> ns_type = grid
>>>>
>>>> ;Reaction field
>>>> rlist = 0.8
>>>> coulombtype = Reaction-field
>>>> rcoulomb = 1.4
>>>> epsilon_r = 1.0
>>>> epsilon_rf = 4.8
>>>> vdwtype = cut-off
>>>> rvdw = 1.4
>>>>
>>>> ; temperature coupling
>>>> Tcoupl = v-rescale
>>>> tc-grps = CHCL3
>>>> tau_t = 0.05
>>>> ld_seed = -1
>>>> ref_t = 300
>>>>
>>>> ; Energy monitoring
>>>> energygrps = CHCl3
>>>>
>>>> ; Isotropic pressure
>>>> Pcoupl = no
>>>> Pcoupltype = isotropic
>>>> tau_p = 0.5
>>>> compressibility = 4.5e-5
>>>> ref_p = 1.0
>>>>
>>>> ; Generate velocites is on at 300 K.
>>>> gen_vel = yes
>>>> gen_temp = 300
>>>> gen_seed = -1
>>>>
>>>> constraint_algorithm=lincs
>>>> lincs_order = 4
>>>> lincs-warnangle = 90
>>>> constraints = all-bonds
>>>> ------------------------------------------------------------------------
>>>>
>>>> and of course, for the npt ensemble I just change
>>>> _________________________________________
>>>> Pcouple = berendsen
>>>>
>>>>
>>>> gen_vel = no
>>>> ------------------------------------------------------------------------
>>>>
>>>> Thank you in advance
>>>>
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>>
>>
>
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Nuno Gonçalo Azoia Lopes
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