[gmx-developers] Verlet Algorithm

[Berk Hess]

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
>>> -- 
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>>
>
>