Jason,
do you think that it is fine to read an MD restart file (containing
coordinates, velocities and periodic box information) with ntx=1 if one
is only interested in coordinates and box information? As I said, I did
exactly this and the first 5 frames of the subsequent simulation looked
good to me. Did I just lose the periodic boundary conditions by doing so
(of course I have set ntb=1 also in the subsequent simulation)?
And, yes, with irest=0 velocities _should_ be ignored, as explicitly
stated in the Amber 12 manual. But this is not formulated in the Amber
11 manual. There, however, for ntx=5 it is noted "The velocity
information will only be used if irest=1." which should be clear enough.
I started two equivalent simulations with ntx=5 and irest=0 (and ig=-1,
tempi=300) from the same restart file and _all_ statistics (energy
values) in both mdout files were exactly the same up the step 3000, when
I aborted the test. If velocities had been assigned randomly, the
numbers should have differed already after the first step, right?
Jan-Philip
On 07/04/2012 06:28 PM, Jason Swails wrote:
> If irest=0, no velocities should be used (even if ntx=5). I think you need
> to use ntx=5 so sander/pmemd knows that velocities are present (if there is
> periodic box information). If this is not the case, I think this probably
> needs to be fixed...
>
> All the best,
> Jason
>
> On Wed, Jul 4, 2012 at 11:33 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
>> wrote:
>
>> Hey,
>>
>> I am using sander from Amber 11 and read coordinates and velocities from
>> an MD restart file via ntx=5. However, I want to generate new
>> velocities, i.e. not use the velocities from the restart file. So I set
>> irest=0, ig=-1, tempi=300. But it seems like the velocities from the
>> restart file are not overridden by randomly generated ones. In this
>> case, I had to use ntx=1 (which seems to also work with restart files
>> and not only with plain coordinate files).
>>
>> Is it new in Amber 12 that irest=0 leads to velocities from an MD
>> restart file being ignored? The Amber 12 manual says for this setting
>> "Velocities in the input coordinate file, if any, will be ignored".
>>
>> Thanks,
>>
>> Jan-Philip Gehrcke
>>
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>>
>
>
>
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Received on Wed Jul 04 2012 - 10:00:02 PDT
