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<p>Hi to all,</p>
<p>I'm Elena della Valle, a Ph.D. student coming from la Sapienza
University of Rome.</p>
<p>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:</p>
<p><img src="cid:part1.251A4226.CEFEA2D6@yahoo.it" alt=""></p>
<p> I did this by modifying in the update.c file in gromacs the
update_do_vv_vel and update_do_vv_pos ad follows:</p>
<p> if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)
&& !nFreeze[gf][d])<br>
{<br>
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]);<br>
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]);<br>
v[n][2] = mv1*(mv1*v[n][2] +
0.5*(w_dt*mv2*f[n][2]))+0.5*accel[ga][2]*dt;<br>
<br>
<br>
<br>
//printf("frame %lf \n", mv1);<br>
// printf("frame %d: %lf\t%lf%lf\n", n, v[n][0],
v[n][1], v[n][2]);<br>
}</p>
<p>in the do_update_vv_pos:</p>
<p>if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)
&& !nFreeze[gf][d])<br>
{<br>
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);<br>
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);<br>
xprime[n][2] = mr1*(mr1*x[n][2]+mr2*dt*v[n][2])
+ mr1*0.5*dt*(w_dt*mr2*f[n][2]);<br>
}</p>
<p><br>
</p>
<p>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. <br>
</p>
<p>I want know if you think that this way is correct, if I
implemented in the right way</p>
<p>And Also I would like to know if in the grompp file I have to
modify other parameters (I use a beredensed coupling)<br>
</p>
Thanks in advance <br>
Sorry for bothering you<br>
Best Regards <br>
Elena della Valle
<pre class="moz-signature" cols="72">--
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</pre>
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