do not use the jar option, just use nmropt
On 2/23/14 12:48 PM, Ali M. Naserian-Nik wrote:
> Hi Jason,
>
> Thank you very much for your reply. But I think for constant force pulling,
> I need a linear potential not a parabolic, and r1-r4 must be set to be
> around or smaller than the final displacement (r2a-r2). Is it true? If yes,
> then how I can change value of r4?
>
> An additional question: What is the role of r4a?
>
>
> On Sunday, February 23, 2014, Jason Swails <jason.swails.gmail.com> wrote:
>
>>
>>> On Feb 23, 2014, at 3:16 AM, "Ali M. Naserian-Nik" <
>> naseriannik.gmail.com <javascript:;>> wrote:
>>> Dear Amber users/developers,
>>>
>>> I need to increase the distance between two atoms under constant velocity
>>> and constant force regime. It seems that I must change the values of r4
>> and
>>> r4a in the restraint file depending on the final value of the SMD
>> distance
>>> (r2a) to obtain a parabolic or linear restraint potential. I set these
>>> parameters to my desired values in the restraint file, but the output
>> file
>>> shows that my desired values are ignored by the code and changed to what
>>> the code prefers. Here is an example of my restraint file and its output:
>>>
>>> RST file:
>> ------------------------------------------------------------------
>>> # SMD under constant velocity
>>> &rst iat=379,761, ifvari=1, nstep1=0, nstep2=0, r1=0.0, r2=86.979,
>>> r3=86.979, r4=386.979, r1a=125.997, r2a=220.979, r3a=220.979,
>> r4a=486.979,
>>> rk2=0.125, rk3=0.125, rk2a=0.125, rk3a=0.125, /
>>>
>>>
>>> Output:
>> ------------------------------------------------------------------
>>> Begin reading energy term weight changes/NMR restraints
>>>
>>> WEIGHT CHANGES:
>>> DUMPFREQ 500 0 0.000000 0.000000 0 0
>>>
>>> ** No weight changes given **
>>>
>>> RESTRAINTS:
>>> Requested file redirections:
>>> DISANG = dist.RST
>>> DUMPAVE = F_vs_d
>>> LISTIN = POUT
>>> LISTOUT = POUT
>>> Restraints will be read from file: dist1.RST
>>> Here are comments from the DISANG input file:
>>>
>>> jar option running
>>> ******
>>>
>>> O3' ( 379)-DH ( 761) NSTEP1= 0 NSTEP2=******
>>> R1 = -13.021 R2 = 86.979 R3 = 86.979 R4 = 186.979 RK2 = 0.125 RK3 = 0.125
>>> R1A= 120.979 R2A= 220.979 R3A= 220.979 R4A= 320.979 RK2A= 0.125 RK3A=
>> 0.125
>>> Rcurr: 86.979 Rcurr-(R2+R3)/2: 0.000 MIN(Rcurr-R2,Rcurr-R3): 0.000
>>>
>>> Number of restraints read = 1
>>>
>>> Done reading weight changes/NMR restraints
>>>
>>> ------------------------------------------------------------------
>>>
>>>
>>> I use Amber12 with all patches applied. Is there a mistake in my input
>> file
>>> or it is a bug?
>>> I'd be so grateful if anyone could help me on these issues.
>> No bug and no mistake, it's simply how the steered md code behaves. The r4
>> variable is adjusted to make sure the potential is always parabolic.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
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>> AMBER.ambermd.org <javascript:;>
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Sun Feb 23 2014 - 10:00:04 PST
