[gmx-developers] Velocities to start leapfrog

[hess at sbc.su.se]

Hi,

Velocity generation is independent of coordinates and time,
except when using constraints.
With constraints the initial velocities are corrected for
the constraints my mdrun in do_shakefirst in src/mdlib/sim_util.c.

Berk

> Dear David,
>
> Thank you very much for your reply.
>
> I though that the velocities generated in that routine were the
> corresponding velocities at time t0 (not shifted to t0-dt/2 yet).
>
> Best regards,
>
> Pablo.
>
> On Jan 18, 2010, at 8:31 AM, David van der Spoel wrote:
>
>> On 1/17/10 11:28 PM, Pablo Campomanes wrote:
>>> Dear gmx-developers,
>>>
>>> After having a look to gromacs source code for quite a long time, I
>>> am
>>> still wondering in where initial velocities generated using the
>>> grompp
>>> utility (I assume v(t0)) are shifted to v(t0 - dt/2) in order to
>>> start
>>> the leap-frog algorithm in "update.c"
>>>
>>> Could anybody shed some light in this issue?
>>
>>
>> src/gmxlib/random.c, routine:
>> void maxwell_speed(real tempi,int seed,gmx_mtop_t *mtop, rvec v[])
>>
>>>
>>> Thanks in advance for your help,
>>>
>>> Pablo
>>>
>>> _____________________________________________
>>> Pablo Campomanes
>>> Laboratory of Computational Chemistry and Biochemistry
>>> BCH 4118 EPF Lausanne
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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