[gmx-users] Essential Dynamics Sampling (EDS) MD

[Lars Schaefer]

Hi Ran,
ok, that's strange. did you try to run it in double prec?
Lars

Ran Friedman wrote:

>Dear Lars, GMX users:
>
>It doesn't seem to be the problem, as the initial RMSD from reference
>structure =    0.16037 nm
>I also get:
>
>Large VCM(group rest):          nan,          nan,          nan,
>ekin-cm:          nan
>
>In the log file.
>
>Ran.
>
>Lars Schaefer wrote:
>  
>
>>Dear Ran,
>>this could mean that you have problems fitting to your reference
>>structure.
>>Lars
>>
>>Ran Friedman wrote:
>>
>>    
>>
>>>Dear all,
>>>
>>>I'm resending this message (please see below)  with some additional
>>>info, hoping that someone can at least point me to what I should check.
>>>
>>>I ran the simulation with the -debug flag and got some "nan" values in
>>>mdrun.log:
>>>
>>>dekin = nan, ekin = 175815  vcm = (     nan      nan      nan)
>>>mv = (     nan      nan      nan)
>>>PC: pres (3x3):
>>>  PC: pres[    0]={         nan,          nan,          nan}
>>>  PC: pres[    1]={         nan,          nan,          nan}
>>>  PC: pres[    2]={         nan,          nan,          nan}
>>>PC: ekin (3x3):
>>>  PC: ekin[    0]={         nan,          nan,          nan}
>>>  PC: ekin[    1]={         nan,          nan,          nan}
>>>  PC: ekin[    2]={         nan,          nan,          nan}
>>>PC: vir  (3x3):
>>>  PC: vir [    0]={ 5.66646e+04,  1.12632e+02, -1.88577e+03}
>>>  PC: vir [    1]={ 5.10852e+02,  5.71922e+04,  3.69013e+03}
>>>  PC: vir [    2]={-1.82055e+03,  3.43891e+03,  6.20980e+04}
>>>PC: box  (3x3):
>>>  PC: box [    0]={ 9.73688e+00,  0.00000e+00,  0.00000e+00}
>>>  PC: box [    1]={ 3.24470e+00,  9.11683e+00,  0.00000e+00}
>>>  PC: box [    2]={-3.24470e+00,  4.55842e+00,  7.97596e+00}
>>>fshift after SR (27x3):
>>>  fshift after SR[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>>>  fshift after SR[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>>>  fshift after SR[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>>>  fshift after SR[    3]={         nan,          nan,          nan}
>>>  fshift after SR[    4]={         nan,          nan,          nan}
>>>
>>>What am I missing?
>>>
>>>Ran Friedman wrote:
>>> 
>>>
>>>      
>>>
>>>>Dear all,
>>>>
>>>>I'm trying to run MD with ED sampling. The target structure is a
>>>>protein
>>>>taken from one simulation, the .tpr file is taken from a different one.
>>>>I'm using a subset of the CA atoms to calculate the eigenvectors. The
>>>>problem is that the MD run crashes after set-up.
>>>>
>>>>Depending on the machine, it either crashes without any error
>>>>message or
>>>>complains about "Too many iterations in routine JACOBI".
>>>>
>>>>Any suggestions?
>>>>
>>>>Thanks,
>>>>Ran.
>>>>        
>>>>
>
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