[gmx-developers] Verlet Algorithm
Berk Hess
hess at kth.se
Thu Oct 6 12:03:30 CEST 2016
do_update_vv_vel() is called twice during each step at different points.
Thus the updates for F(t) and F(t+dt) are done separately.
Berk
On 2016-10-06 11:53, Elena della Valle wrote:
>
> The question is that on the gromacs manual I read that the verlet
> algorithm for the velocity corresponds to , now in the gromacs code in
> the verlet part I don't find the corresponds for the term [1/2*(∆t/m)*
> F(t + ∆t)], is not implemented?
>
> Sorry if I'm not so clear
>
> Thanks
>
> Elena della Valle
>
>
> Il 06/10/2016 11:39, Berk Hess ha scritto:
>> I don't understand our question.
>> accel[ga] is a fixed acceleration per atom for non-equilibrium
>> dynamics. This will be 0, unless you are doing non-equilibrium
>> dynamics. You can ignore or remove this term, since you will not need
>> it.
>>
>> Cheers,
>>
>> Berk
>>
>> On 2016-10-06 11:25, Elena della Valle wrote:
>>>
>>> Okey but in the update.c file line 300, in the following equation :
>>> v[n][d] = mv1*(mv1*v[n][d] +
>>> 0.5*(w_dt*mv2*f[n][d]))+0.5*accel[ga][d]*dt;
>>> with the term "0.5*accel[ga][d]*dt" it corresponds to the term
>>> "[1/2*(∆t/m)* F(t + ∆t)] " in the verlet algorithm ?
>>> Thanks in advance for helping me
>>> Best Regards
>>> Elena della Valle
>>>
>>> Il 06/10/2016 09:30, Berk Hess ha scritto:
>>>> Hi,
>>>>
>>>> I guess you mean ga = cACC[n].
>>>> cACC[n] contains the acceleration group index for atom n. This is
>>>> for non-equilibrium dynamics where groups of atom are accelerated.
>>>> (apologies for the cryptic notation without documentation)
>>>>
>>>> Cheers,
>>>>
>>>> Berk
>>>>
>>>> On 2016-10-06 07:44, Elena Della valle wrote:
>>>>> Hi, I have just a last question what gromacs means exactly with
>>>>> the term: cACC[ga]?
>>>>> Thanks in advance
>>>>> Best Regards
>>>>> Elena della Valle
>>>>>
>>>>>
>>>>>
>>>>>> Il giorno 04 ott 2016, alle ore 17:58, Berk Hess <hess at kth.se> ha
>>>>>> scritto:
>>>>>>
>>>>>>> On 10/04/2016 05:36 PM, David van der Spoel wrote:
>>>>>>>> On 04/10/16 17:00, Elena Della valle wrote:
>>>>>>>> I used the gromacs 4.6.5
>>>>>>>> Best regards
>>>>>>>> Elena della Valle
>>>>>>> Crudely put we do not support that version anymore, so if you
>>>>>>> would like to have this considered for inclusion in gromacs you
>>>>>>> would have to implement it in the master branch and upload it to
>>>>>>> gerrit. Whether it is correct you should test your self using
>>>>>>> some known cases and carefully constructed inputs.
>>>>>> In addition, even when you are not interested in contributing the
>>>>>> code, all developer work with the most recent versions, so it's
>>>>>> easier for us to help you with the master version, especially for
>>>>>> code that has changed a lot over the past years like the Velocity
>>>>>> Verlet integrator. (And I think anyone should prefer the latest
>>>>>> version for development, so one doesn't end up with functionality
>>>>>> that only works in 5 year old code.)
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Berk
>>>>>>> Maybe you can also answer the question when a magnetic effect
>>>>>>> would be important?
>>>>>>>>
>>>>>>>>>> Il giorno 04 ott 2016, alle ore 16:49, David van der Spoel
>>>>>>>>>> <spoel at xray.bmc.uu.se> ha scritto:
>>>>>>>>>>
>>>>>>>>>> On 04/10/16 15:15, Elena della Valle wrote:
>>>>>>>>>>
>>>>>>>>>> Hi to all,
>>>>>>>>>>
>>>>>>>>>> I'm Elena della Valle, a Ph.D. student coming from la Sapienza
>>>>>>>>>> University of Rome.
>>>>>>>>>>
>>>>>>>>>> I'm writing because I have some questions about some
>>>>>>>>>> modifications that
>>>>>>>>>> I have done to the update of velocities and positions in the
>>>>>>>>>> verlet
>>>>>>>>>> algorithm. My aim is to implement the magnetic field in
>>>>>>>>>> gromacs by
>>>>>>>>>> introducing the therm of the larmor frequency to the
>>>>>>>>>> velocities and
>>>>>>>>>> positions. By literature I read that this has been done by
>>>>>>>>>> the update of
>>>>>>>>>> the verlet velocities and positions with the frequency larmor
>>>>>>>>>> therm.
>>>>>>>>>> These are the equations in order to be more clear on what i
>>>>>>>>>> wanted to do:
>>>>>>>>>>
>>>>>>>>>> I did this by modifying in the update.c file in gromacs the
>>>>>>>>>> update_do_vv_vel and update_do_vv_pos ad follows:
>>>>>>>>>>
>>>>>>>>>> if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) &&
>>>>>>>>>> !nFreeze[gf][d])
>>>>>>>>>> {
>>>>>>>>>> v[n][0] = mv1*(mv1*v[n][0] +
>>>>>>>>>> 0.5*(w_dt*mv2*f[n][0]))+0.5*accel[ga][0]*dt +
>>>>>>>>>> w_dt*charge[n]*campoB*v[n][1]*mv1*mv1 +
>>>>>>>>>> 0.25*dt*invmass[n]*charge[n]*campoB*((w_dt*mv2*mv1*f[n][1]) +
>>>>>>>>>> accel[ga][1]*dt -2*w_dt*charge[n]*campoB*mv1*mv1*v[n][0]);
>>>>>>>>>> v[n][1] = mv1*(mv1*v[n][1] +
>>>>>>>>>> 0.5*(w_dt*mv2*f[n][1]))+0.5*accel[ga][1]*dt +
>>>>>>>>>> w_dt*charge[n]*campoB*v[n][0]*mv1*mv1 -
>>>>>>>>>> 0.25*dt*invmass[n]*charge[n]*campoB*((w_dt*mv2*mv1*f[n][0]) +
>>>>>>>>>> accel[ga][0]*dt +2*w_dt*charge[n]*campoB*mv1*mv1*v[n][1]);
>>>>>>>>>> v[n][2] = mv1*(mv1*v[n][2] +
>>>>>>>>>> 0.5*(w_dt*mv2*f[n][2]))+0.5*accel[ga][2]*dt;
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> //printf("frame %lf \n", mv1);
>>>>>>>>>> // printf("frame %d: %lf\t%lf%lf\n", n, v[n][0],
>>>>>>>>>> v[n][1],
>>>>>>>>>> v[n][2]);
>>>>>>>>>> }
>>>>>>>>>>
>>>>>>>>>> in the do_update_vv_pos:
>>>>>>>>>>
>>>>>>>>>> if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) &&
>>>>>>>>>> !nFreeze[gf][d])
>>>>>>>>>> {
>>>>>>>>>> xprime[n][0] =
>>>>>>>>>> mr1*(mr1*x[n][0]+mr2*dt*v[n][0]) +
>>>>>>>>>> mr1*0.5*dt*(w_dt*mr2*f[n][0] +
>>>>>>>>>> w_dt*charge[n]*campoB*v[n][1]*mr1);
>>>>>>>>>> xprime[n][1] =
>>>>>>>>>> mr1*(mr1*x[n][1]+mr2*dt*v[n][1]) +
>>>>>>>>>> mr1*0.5*dt*(w_dt*mr2*f[n][1] -
>>>>>>>>>> w_dt*charge[n]*campoB*v[n][0]*mr1);
>>>>>>>>>> xprime[n][2] =
>>>>>>>>>> mr1*(mr1*x[n][2]+mr2*dt*v[n][2]) +
>>>>>>>>>> mr1*0.5*dt*(w_dt*mr2*f[n][2]);
>>>>>>>>>> }
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> After that in the grompp file I modified the integrator in
>>>>>>>>>> md-vv and I
>>>>>>>>>> run the simulation and it seems to use the position and
>>>>>>>>>> velocities
>>>>>>>>>> modifications.
>>>>>>>>>>
>>>>>>>>>> I want know if you think that this way is correct, if I
>>>>>>>>>> implemented in
>>>>>>>>>> the right way
>>>>>>>>>>
>>>>>>>>>> And Also I would like to know if in the grompp file I have to
>>>>>>>>>> modify
>>>>>>>>>> other parameters (I use a beredensed coupling)
>>>>>>>>>>
>>>>>>>>>> Thanks in advance
>>>>>>>>>> Sorry for bothering you
>>>>>>>>>> Best Regards
>>>>>>>>>> Elena della Valle
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Elena della Valle
>>>>>>>>>> Ph.D. Student in Electronic Engineering
>>>>>>>>>>
>>>>>>>>>> Department of Information Engineering, Electronics and
>>>>>>>>>> Telecommunications
>>>>>>>>>> Sapienza, University of Rome
>>>>>>>>>> via Eudossiana, 18 00184 Rome
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> Just a quick question: which version did you use? All
>>>>>>>>> development should be in the master version and this looks
>>>>>>>>> like uses something older.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>>>>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>>>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>>>>>>>>> --
>>>>>>>>> Gromacs Developers mailing list
>>>>>>>>>
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>>>>>>>
>>>>>> --
>>>>>> Gromacs Developers mailing list
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>>>>
>>>
>>
>
> --
> Elena della Valle
> Ph.D. Student in Electronic Engineering
>
> Department of Information Engineering, Electronics and Telecommunications
> Sapienza, University of Rome
> via Eudossiana, 18 00184 Rome
>
>
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