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

[Ran Friedman]

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.