[gmx-users] Pressure very high with chloroform and gromacs-4.5.5
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Oct 13 00:21:23 CEST 2011
On 13/10/2011 12:35 AM, Nuno Azoia wrote:
> 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.
Your chloroform parameters are probably only valid for a condensed
phase, and your initial density is nowhere near that. Please follow the
approach here
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation.
>
> 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.
Shrug. Without command lines and descriptions of what is in your input,
we are helpless. Please follow the above advice.
>
> 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.
No, the implementation of parallelization might have an effect here if
you were starting from a reasonable approximation of a condensed phase.
These two observations are just two of the possible things that could
happen to a liquid at extremely low density.
Mark
>
> 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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