See if it can warm up without problems. What do you have to lose?
Bill
On 8/25/17 8:19 AM, Chayya Bhargac wrote:
> I did try starting MD again and it does work but the minimization doesn't go
> to completion again.
>
> When I start again it completes 100 steps out of 2000 steps.
>
> Does this mean it is already minimizer? Would it be a good
> idea to proceed to equilibration with this structure?
>
>
>
> Thanks,
> Chayya B.
>
> On Fri, Aug 25, 2017 at 2:10 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> With 10K dynamics, you will find a lower minimum, I'll bet. Try ignoring
>> it, and see if you have any problems starting md.
>>
>> Bill
>>
>>
>> On 8/24/17 11:05 PM, Chayya Bhargac wrote:
>>> Dear Amber users,
>>>
>>>
>>> I am trying to perform a minimization for a system set up with POL3
>>> water box and ff02 force fields. It has 24 Ca2+ and 20 Cl- ions.
>>>
>>> While performing a restrained minimization with the code below, I get a
>>> LINMIN error. From previous posts in the mailing list, people have
>>> continued with their simulations despite the error. But in my case, the
>>> minimization stops completely. The minimization which has 4000 steps,
>> stops
>>> in 200 steps. If this is because of bad contacts, what can I do to remove
>>> it? Is there any way to proceed after this?
>>>
>>>
>>> Minimization code:
>>>
>>> Minimization with Cartesian restraints for the solute
>>>
>>> &cntrl
>>>
>>> imin=1, maxcyc=400, ncyc=100, ntc=2, ipol=1,
>>>
>>> ntpr=50, ntr=1
>>>
>>> $end
>>>
>>> Group input for restrained atoms
>>>
>>> 500.0
>>>
>>> RES 1 172
>>>
>>> END
>>>
>>> END
>>>
>>>
>>> Error:
>>>
>>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>>
>>>
>>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>>
>>>
>>>
>>> NSTEP ENERGY RMS GMAX NAME
>> NUMBER
>>> 200 -3.5241E+05 1.9021E+01 1.6012E+02 HD12 53
>>>
>>>
>>> BOND = 69.5447 ANGLE = 457.3107 DIHED =
>>> 1518.5396
>>>
>>> VDWAALS = 86424.7986 EEL = -358147.2457 HBOND =
>>> 0.0000
>>>
>>> 1-4 VDW = 690.4683 1-4 EEL = 8524.4425 RESTRAINT =
>>> 397.4833
>>>
>>> EPOLAR = -92346.4873
>>>
>>> EAMBER = -352808.6287
>>>
>>> Dipole convergence: rms = 0.560E-01 temperature = 0.00
>>>
>>>
>>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>>
>>>
>>> ***** REPEATED LINMIN FAILURE *****
>>>
>>>
>>>
>>>
>>> Thank you,
>>> Chayya B.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
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Received on Fri Aug 25 2017 - 10:00:02 PDT
