[gmx-developers] Verlet Algorithm
Berk Hess
hess at kth.se
Thu Oct 6 11:39:43 CEST 2016
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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>>>>>
>>>> --
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