[gmx-developers] Verlet Algorithm
Elena della Valle
elena.dv46 at yahoo.it
Wed Mar 1 18:22:54 CET 2017
> Hi, sorry if I bother you again with the velocity verlet algorithm,
> but I have another question, in the Gromacs Manual for the Velocity
> verlet algorithm for the position is written that r (t + deltaT) is
> equal to:
>
> But if I look in the gromacs code, in the update.cpp file I see that
> the position for the verlet algorithm the update of the positions is
> due as:
>
>
>
> and I don't see the therm of the Force multiplied for deltaT^2/2*m, is
> because in the code the therm v[n] is interpreted as v(t + delta)?
> thanks in advance
> Best Regards
> Elena della Valle
>
>
>
> Il 06/10/2016 12:03, Berk Hess ha scritto:
>> 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
>>>
>>>
>>
>>
>>
>
> --
> 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
--
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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