[gmx-users] Re: density profile

[Dr. Vitaly Chaban]

Justin  -

I am sure mdrun reads coordinates from -cpi state.cpt ....

Vitaly




On Mon, Apr 1, 2013 at 7:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
>
> On Mon, Apr 1, 2013 at 1:29 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
>
>> It is something very new for me.
>>
>> If structure, etc are not read from CPT files, why does one need them
>> for...
>>
>
> I just tested and verified that -c is required, even in the presence of -t
> passing a .cpt file. I suspect that the rationale is that the .cpt file is
> used for state variables, velocities, etc (i.e. an upgrade over the very
> old mechanism of passing a .trr to -t and .edr to -e).  It would certainly
> make sense if the coordinates from the .cpt were read, but I don't know if
> doing so present a substantial improvement over using a coordinate file to
> -c.
>
> -Justin
>
>
>>
>>
>
>> On Mon, Apr 1, 2013 at 7:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>>
>>> On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
>>>
>>>> I think if you use checkpoint files, the program does not read either
>>>> MDP,
>>>> or GRO, or TOP, or anything except CPT.
>>>>
>>>>
>>>>
>>> I would have to check the code to be sure, but that is certainly not
>>> true in the case of the .mdp file.  That is always read.  I want to say
>>> that the coordinate file is required as well, though that would be an easy
>>> test using grompp.  It should be easy to track the box vectors from the
>>> .edr file to see what the initial value was, to see if it came from the
>>> .cpt or .gro file.  Likely from the .cpt file.
>>>
>>> -Justin
>>>
>>> --
>>>
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>>
>>>
>>>
>>
>
>
> --
>
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>