Dear Adrian,
Thanks very much and now I understand why a "force constant" is needed in the restraint.
Sincerely yours
Xing
On 08/15/2017 11:22 AM, Adrian Roitberg wrote:
> Hi XIng
>
> The amber16 manual says:
>
> "The output file differs substantially from that used in the case of nmr
> restraints. It contains 4 columns: x0(t), x,
> force, work. Here work is computed as the integrated force over
> distances (or angle, or torsion)."
>
>
> So, the first column is the value of the coordinate you WANT the system
> to have a particular time, interpolated between the initial and final
> values by nstep/nstlim
>
> The second column is the ACTUAL value of the coordinate at that same time.
>
> Adrian
>
>
> On 8/14/17 10:08 PM, Xing wrote:
>> Dear Dr. Roitberg,
>>
>> I'm just starting using SMD. Now I understand that the first column is
>> distance (in Angstrom?), but what is the second column? I cannot find it
>> in the manual....
>>
>> Thanks and best wishes,
>> Xing
>>
>> On 05/07/2016 07:33 PM, Adrian Roitberg wrote:
>>> Hi Collin
>>>
>>> Indeed, the third column is force (vs t). The units are neither kcal/mol
>>> nor piconewtons.
>>>
>>>
>>> kcal/mol is a unit of energy not force.
>>>
>>> The correct units are (kcal/mol)/Angstrom
>>>
>>> On 5/6/16 5:08 PM, Nisler, Collin R. wrote:
>>>> Hello, I ran a steered molecular dynamics simulation using jar=1, and now have the dist_vs_t file. I am fairly certain that the third column of this file is the force of pulling at each step, but I am uncertain what its units are. Is this in kcal/mol, or in piconewtons? Thanks very much.
>>>>
>>>>
>>>> Collin Nisler
>>>>
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Received on Tue Aug 15 2017 - 17:30:02 PDT
