[gmx-users] Problem with OpenMP+MPI

[jesmin jahan]

Thanks Justin.
Well, I am felling stupid now! Could you kindly provide me some better
.mdp parameters that make more sense?

gromacs 4.6 gives me error with my previous parameters which were
working perfect in gromacs 4.5.3

It says we have to use cut-off verlet, either we have to use coupling
temp or we have to set verlet-buffer-drift = -1.
Then it says set pbc to xyz or xy. I tried to change my rlist or other
cutoff values. It says box is too large or small.

So, i am really very confused!
It will be very kind of you, if you can suggest me some parameters
which match best with my previous parameters namely:


>> constraints         =  none
>> integrator          =  md
>> pbc                 =  no
>> dt                  =  0.001
>> nsteps              =  0
>> rcoulomb            = 300
>> rvdw                = 300
>> rlist               = 300
>> nstgbradii          = 300
>> rgbradii            = 300
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  HCT ;
>> sa_algorithm        =  None
>> gb_dielectric_offset    = 0.02
>>
>> optimize_fft             = yes
>> energygrps               = protein
-----------------------------

Thanks a lot for your help,
Jesmin
On Wed, Feb 27, 2013 at 10:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/27/13 10:01 AM, jesmin jahan wrote:
>>
>> Hi Justin,
>>
>> Thanks for your reply.
>>
>> I am able to run it now. I am using the following parameters.
>>
>> --------------------------------------------------------------------------------------------------------------
>> constraints         =  none
>> integrator          =  md
>> cutoff-scheme       = Verlet
>> pbc                 =  xyz
>> verlet-buffer-drift = -1
>> dt                  =  0.001
>> nsteps              =  0
>> rcoulomb            = 1
>> rvdw                = 1
>> rlist               = 1
>> nstgbradii          = 1
>> rgbradii            = 1
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  HCT ;
>> sa_algorithm        =  None
>> gb_dielectric_offset    = 0.02
>>
>> optimize_fft             = yes
>> energygrps               = protein
>>
>>
>> --------------------------------------------------------------------------------------------
>> I got the following energy values for this run.
>> Statistics over 1 steps using 1 frames
>>
>>     Energies (kJ/mol)
>> GB Polarization        LJ (SR)   Coulomb (SR)      Potential    Kinetic
>> En.
>>     -1.52255e+05    5.75419e+08   -2.44085e+05    5.75023e+08
>> 6.36555e+11
>>     Total Energy    Temperature Pressure (bar)
>>      6.37130e+11    1.60603e+10    7.90024e+10
>>
>>
>>
>> ###############################################################################
>> On the other hand, when I used gromacs-4.5.3, with the following
>> parameters:
>>
>> -----------------------------------------------------------------------------------------------------------------------------------------
>> constraints         =  none
>> integrator          =  md
>> pbc                 =  no
>> dt                  =  0.001
>> nsteps              =  0
>> rcoulomb            = 300
>> rvdw                = 300
>> rlist               = 300
>> nstgbradii          = 300
>> rgbradii            = 300
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  HCT ;
>> sa_algorithm        =  None
>> gb_dielectric_offset    = 0.02
>>
>> optimize_fft             = yes
>> energygrps               = protein
>>
>> --------------------------------------------------------------------------------------
>> I got the following energy values:
>>
>>    Energies (kJ/mol)
>> GB Polarization        LJ (SR)   Coulomb (SR)      Potential    Kinetic
>> En.
>>     -1.58040e+04    0.00000e+00   -2.42022e+05   -2.57826e+05
>> 0.00000e+00
>>     Total Energy    Temperature Pressure (bar)
>>     -2.57826e+05    0.00000e+00    0.00000e+00
>>
>>
>> You can see that there is a huge difference (10 times), in these two
>> energy values!
>>
>> How can I get a similar value that I was receiving previously (i.e.,
>> -1.58040e+04)? The previous energy was correct, while the current
>> value is 10 times more than the previous one.
>>
>
> Also note that your temperature is about a thousand times hotter than a
> nuclear explosion, as well :)
>
> You're comparing dissimilar things in the two setups and expecting them to
> come out the same.  With 4.6, you're using PBC and explicit cutoffs, in a
> box that's likely inappropriate as you have massive atomic overlap (which is
> what gives rise to the ridiculous temperature).  In the case of 4.5.3 you
> have a non-periodic system and thus you can't get overlap between images
> (because there are none).  Conclusion: your settings for 4.6 simply don't
> make sense.
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.