[gmx-developers] Velocities to start leapfrog

[Pablo Campomanes]

Hi Berk,

It was exactly the information I was looking for. 
Thanks a lot.

Best regards,

Pablo.


On Jan 18, 2010, at 10:23 AM, hess at sbc.su.se wrote:

> 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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