On 07/04/2012 06:46 PM, Jan-Philip Gehrcke wrote:
> 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)?
>
In order to make it easier to answer this, I provide here the
corresponding part of the mdout file:
> &cntrl
> ntx = 1,
> irest = 0,
> ntb = 1,
> cut = 8.0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 1,
> tautp = 10.0,
> nstlim = 2000000,
> dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 10000,
> ioutfm = 1,
> ig = -1,
> jar = 1,
> /
[...]
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 33.405
> | New format PARM file being parsed.
"getting new box info from bottom of inpcrd" and "peek_ewald_inpcrd: Box
info found" are promising, right? Looks like the box info has been read
although ntx is 1 and not 5.
> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 04 2012 - 10:00:03 PDT
