Re: Am I doing the Right Thing?

From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jul 12 2012 - 22:44:49 CDT

yep that is exactly right.

On Thu, Jul 12, 2012 at 7:00 PM, Roy Fernando <roy.nandos_at_gmail.com> wrote:

> Hi Aron,
>
> I understand now what you are saying.
> Following is just to double check.
> Once we have equilibrated the system we can make a pdb file for the system
> and continue to use that pdb file as the coordinate file for any restart
> simulation. As long as we use binary inputs from the previous simulation,
> it is not essential to make a new pdb file after each simulation for the
> restart.The values in the pdb file do not really matter to the simulation
> as the simulation pick up starting values from the binary
> restart.coordinate file. Is that what you are saying?
>
> These kind of clarifications make me understand my simulations better.
> Thanks again.
>
> Roy
>
>
>
> On Thu, Jul 12, 2012 at 1:36 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>
>> yes, I think that will work fine. My only point from before is that you
>> can use:
>>
>> coordinates NE2_wb.pdb (I'm guessing that is the name of the first
>> coordinate file you used to begin your simulations)
>>
>> and keep using that for all subsequent restarts, thereby avoiding having
>> to do the VMD thing, since the coordinates are only used to get atom names
>> and such, whereas the actual x,y,z values come from bincoordinates.
>>
>> ~Aron
>>
>>
>> On Thu, Jul 12, 2012 at 1:31 PM, Roy Fernando <roy.nandos_at_gmail.com>wrote:
>>
>>> Hi Aron,
>>>
>>> Thanks for the message. Yes I am using binary inputs.
>>> For example my restart configuration file will look like the following.
>>>
>>> structure NE2_wb.psf
>>> coordinates NE2_wb_eq1.pdb
>>> bincoordinates NE2_eq1_data.restart.coor
>>> binvelocities NE2_eq1_data.restart.vel
>>> extendedSystem NE2_eq1_data.restart.xsc
>>>
>>> So I am fine, is that what you say?
>>>
>>> Roy
>>>
>>> On Thu, Jul 12, 2012 at 1:10 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>>>
>>>> are you using binary inputs? If not, then you should just be using the
>>>> restart coordinate file as your input for the next window. If you are
>>>> using binary coordinates, then you are supplying the coordinates from the
>>>> restart as "bincoordinates", and for "coordinates" you are just suppling
>>>> the pdb you used for the first window, as the actual coordinates in it
>>>> don't matter. You can also do what you are doing, it will work fine
>>>> (assuming we are talking about binary coordinates here), but it's not
>>>> necessary to do that re-writing every time.
>>>>
>>>>
>>>> On Thu, Jul 12, 2012 at 1:02 PM, Roy Fernando <roy.nandos_at_gmail.com>wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I have a question to ask, just to verify if I am doing the right thing.
>>>>> I am doing a TCL force simulation in segments. I need to study short
>>>>> time scale effects to the structure under the action of the external forces
>>>>> (Defined in the TCL script).
>>>>>
>>>>> So I run the simulation, say for 1000 time steps. Then, I need to
>>>>> restart the simulation with the structure produced at the end of the first
>>>>> part. In the restart configuration file I can use the restart files
>>>>> generated in the first part. But I also need a pdb coordinate file.
>>>>>
>>>>> To generate that coordinate file, I load the restart.coor file on to
>>>>> the system psf file in VMD and just write a pdb file for that. This pdb
>>>>> file I am using as the coordinate file in the restart simulation. Is this
>>>>> the correct methodology?
>>>>>
>>>>> I appreciate your input
>>>>>
>>>>> Roy
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Aron Broom M.Sc
>>>> PhD Student
>>>> Department of Chemistry
>>>> University of Waterloo
>>>>
>>>>
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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