> My energy value at the first step of the second
minimization(Minimizing the whole system), E=-4.3501E+05, is not equal
to my energy value at the end of my first minimization step(minimizing
just water), E=-4.3467E+05.
If all the potential-related terms in the two mdin files are the same,
the energy terms should be the same; look at each element, not the sum,
for further clues.
Bill
On 6/14/17 10:20 PM, Ramin Salimi wrote:
> Thanks Bill
>
> So I will be waiting for more insight into this.
>
> Though I have a rather irrelevant question: My energy value at the first step of the second minimization(Minimizing the whole system), E=-4.3501E+05, is not equal to my energy value at the end of my first minimization step(minimizing just water), E=-4.3467E+05. I read in the list that they are supposed to be equal:
>
> http://archive.ambermd.org/201411/0147.html
>
>
> How important is that? while my system did go through the minimization completely successfully, why is that so? All in all, am I fine in regards to the result?
>
> Thanks
>
> Ramin
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Wednesday, June 14, 2017 8:30:49 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Warning during minimization
>
> Hi Ramin,
>
> That leaves grepping the code while waiting for someone in the know to
> arrive.
>
> Bill
>
>
> On 6/14/17 6:28 PM, Ramin Salimi wrote:
>> Hi Bill
>>
>> Thanks for the reply.
>>
>> As I said before, I am also running it without the restraint, and it shows to be going well. But my question is why it is giving the warning due apparently to imposing the restraint? There should not be anything wrong with applying that restraint. Although it is not an error but a warning, why is that so?
>>
>> I just wondered to understand what the warning says.
>>
>> The reason that I am trying to impose the restraint is that I would want to keep the length of the molecule the same; in other words, to keep the two atoms in their positions. I should be able to do so.
>>
>> Ramin
>>
>>
>> ________________________________
>> From: Bill Ross <ross.cgl.ucsf.edu>
>> Sent: Wednesday, June 14, 2017 8:20:07 PM
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Warning during minimization
>>
>> What if you try without restraints? If that works, then worry about the
>> restraints.
>>
>> Also, you could search the code for 'No offset found for match' to get
>> clues.
>>
>> Bill
>>
>>
>> On 6/14/17 6:14 PM, Ramin Salimi wrote:
>>> Dear All
>>>
>>> I am doing my second step of minimization to minimize the whole system but to keep two end atoms fixed. However, I get the following WARNING, but the minimization is still going on, and is printing the output file:
>>>
>>> WARNING **: No offset found for match "n" at page 421 after processing 1 results
>>>
>>> This is my input file to minimize the whole system:
>>> Minimize solute and solvent
>>> &cntrl
>>> imin=1, ntmin=1, nmropt=1,
>>> maxcyc=10000, ncyc=5000,
>>> ntb=1, ntp=0, cut=10.0, nsnb=20,
>>> ntc=1, ntf=1, ntx=1, irest=0,
>>> ntpr=100, ntwr=100,
>>> ioutfm=1, ibelly=0, ntr=0,
>>> iwrap=0, igb=0,
>>>
>>> &end
>>> &wt type='DUMPFREQ', istep1=10 /
>>> &wt type='END' /
>>> DISANG=dist_nmropt.RST
>>> DUMPAVE=dist_vs_nmroptchange
>>> LISTIN=POUT
>>> LISTOUT=POUT
>>> /
>>> where dist_nmropt.RST is:
>>>
>>> &rst
>>> iat=2,382,
>>> r1=0,
>>> r2=44.9179,
>>> r3=44.9179,
>>> r4=9999,
>>> rk2=50.0,
>>> rk3=50.0,
>>>
>>> &end
>>>
>>> I got the value of r2=r3=44.9179 by measuring the distance from the output coordinate file of the first minimization step with CPPTRAJ. I feel it has something to do with using the restraint since with switching off the nmropt option, it has not printed that warning so far. But why does it show the warning with nmropt=1? is it important?
>>>
>>> I would appreciate any help.
>>>
>>> Regards
>>>
>>> Ramin
>>>
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Received on Wed Jun 14 2017 - 23:30:02 PDT
