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

[Lars Schaefer]

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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