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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Generally, velocity verlet is performed the following way (from wikipedia https://en.wikipedia.org/wiki/Verlet_integration)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoNormal" style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt;font-family:Calibri;color:windowtext">Calculate</span><span style="font-size:11.0pt;font-family:Calibri"> v(t+dt/2) = v(t) + dt/2 a(t)<o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt;font-family:Calibri;color:windowtext">Calculate x(t+dt) = x(t) + dt*v(t+dt/2)</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt;font-family:Calibri;color:windowtext">Calculate a(t+dt) from x(t+dt)</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt;font-family:Calibri;color:windowtext">Calculate v(t+dt) = v(t+dt/2) + dt/2 a(t+dt)</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></li></ol>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">After the first step, it’s only one force call per step because you can reuse the force in step 4 in the next step 1.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">The logic is not always clear in the gromacs code, since the bookkeeping needs to be rather complicated to do both leapfrog and velocity.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Michael Shirts<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Associate Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><a href="mailto:michael.shirts@colorado.edu">michael.shirts@colorado.edu</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><a href="http://www.colorado.edu/lab/shirtsgroup/"><span style="text-decoration:none">http://www.colorado.edu/lab/shirtsgroup/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Phone: (303) 735-7860<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Office: JSCBB C123<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Department of Chemical and Biological Engineering<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">University of Colorado Boulder</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se> on behalf of Elena della Valle <elena.dv46@yahoo.it><br>
<b>Reply-To: </b>"gmx-developers@gromacs.org" <gmx-developers@gromacs.org><br>
<b>Date: </b>Wednesday, March 1, 2017 at 12:19 PM<br>
<b>To: </b>"gromacs.org_gmx-developers@maillist.sys.kth.se" <gromacs.org_gmx-developers@maillist.sys.kth.se><br>
<b>Subject: </b>Re: [gmx-developers] Verlet Algorithm<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p>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:<img border="0" width="297" height="51" id="_x0000_i1025" src="cid:image001.png@01D292CF.4A8C25F0"><o:p></o:p></p>
<p>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:<o:p></o:p></p>
<p><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><img border="0" width="413" height="16" id="_x0000_i1026" src="cid:image002.png@01D292CF.4A8C25F0"><br>
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)?<br>
thanks in advance<br>
Best Regards <br>
Elena della Valle<br>
<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">Il 06/10/2016 12:03, Berk Hess ha scritto:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">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.<br>
<br>
Berk<br>
<br>
On 2016-10-06 11:53, Elena della Valle wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p>The question is that on the gromacs manual I read that the verlet algorithm for the velocity corresponds to
<img border="0" width="268" height="36" id="_x0000_i1027" src="cid:image003.png@01D292CF.4A8C25F0">, 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?<o:p></o:p></p>
<p>Sorry if I'm not so clear <o:p></o:p></p>
<p>Thanks <o:p></o:p></p>
<p>Elena della Valle<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Il 06/10/2016 11:39, Berk Hess ha scritto:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">I don't understand our question. <br>
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.
<br>
<br>
Cheers, <br>
<br>
Berk <br>
<br>
On 2016-10-06 11:25, Elena della Valle wrote: <br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><br>
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;
<br>
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 ?
<span style="font-family:PMingLiU"><br>
</span>Thanks in advance for helping me <span style="font-family:PMingLiU"><br>
</span>Best Regards <span style="font-family:PMingLiU"><br>
</span>Elena della Valle <span style="font-family:PMingLiU"><br>
<br>
</span>Il 06/10/2016 09:30, Berk Hess ha scritto: <br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi, <br>
<br>
I guess you mean ga = cACC[n]. <br>
cACC[n] contains the acceleration group index for atom n. This is for non-equilibrium dynamics where groups of atom are accelerated.
<br>
(apologies for the cryptic notation without documentation) <br>
<br>
Cheers, <br>
<br>
Berk <br>
<br>
On 2016-10-06 07:44, Elena Della valle wrote: <br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi, I have just a last question what gromacs means exactly with the term: cACC[ga]?
<br>
Thanks in advance <br>
Best Regards <br>
Elena della Valle <br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Il giorno 04 ott 2016, alle ore 17:58, Berk Hess <a href="mailto:hess@kth.se">
<hess@kth.se></a> ha scritto: <br>
<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">On 10/04/2016 05:36 PM, David van der Spoel wrote: <br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">On 04/10/16 17:00, Elena Della valle wrote: <br>
I used the gromacs 4.6.5 <br>
Best regards <br>
Elena della Valle <o:p></o:p></p>
</blockquote>
<p class="MsoNormal">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. <o:p></o:p></p>
</blockquote>
<p class="MsoNormal">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.)
<br>
<br>
Cheers, <br>
<br>
Berk <br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Maybe you can also answer the question when a magnetic effect would be important?
<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-bottom:12.0pt">Il giorno 04 ott 2016, alle ore 16:49, David van der Spoel
<a href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a> ha scritto: <br>
<br>
On 04/10/16 15:15, Elena della Valle wrote: <br>
<br>
Hi to all, <br>
<br>
I'm Elena della Valle, a Ph.D. student coming from la Sapienza <br>
University of Rome. <br>
<br>
I'm writing because I have some questions about some modifications that <br>
I have done to the update of velocities and positions in the verlet <br>
algorithm. My aim is to implement the magnetic field in gromacs by <br>
introducing the therm of the larmor frequency to the velocities and <br>
positions. By literature I read that this has been done by the update of <br>
the verlet velocities and positions with the frequency larmor therm. <br>
These are the equations in order to be more clear on what i wanted to do: <br>
<br>
I did this by modifying in the update.c file in gromacs the <br>
update_do_vv_vel and update_do_vv_pos ad follows: <br>
<br>
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) <br>
{ <br>
v[n][0] = mv1*(mv1*v[n][0] + <br>
0.5*(w_dt*mv2*f[n][0]))+0.5*accel[ga][0]*dt + <br>
w_dt*charge[n]*campoB*v[n][1]*mv1*mv1 + <br>
0.25*dt*invmass[n]*charge[n]*campoB*((w_dt*mv2*mv1*f[n][1]) + <br>
accel[ga][1]*dt -2*w_dt*charge[n]*campoB*mv1*mv1*v[n][0]); <br>
v[n][1] = mv1*(mv1*v[n][1] + <br>
0.5*(w_dt*mv2*f[n][1]))+0.5*accel[ga][1]*dt + <br>
w_dt*charge[n]*campoB*v[n][0]*mv1*mv1 - <br>
0.25*dt*invmass[n]*charge[n]*campoB*((w_dt*mv2*mv1*f[n][0]) + <br>
accel[ga][0]*dt +2*w_dt*charge[n]*campoB*mv1*mv1*v[n][1]); <br>
v[n][2] = mv1*(mv1*v[n][2] + <br>
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], <br>
v[n][2]); <br>
} <br>
<br>
in the do_update_vv_pos: <br>
<br>
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]) + <br>
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]) + <br>
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]) + <br>
mr1*0.5*dt*(w_dt*mr2*f[n][2]); <br>
} <br>
<br>
<br>
After that in the grompp file I modified the integrator in md-vv and I <br>
run the simulation and it seems to use the position and velocities <br>
modifications. <br>
<br>
I want know if you think that this way is correct, if I implemented in <br>
the right way <br>
<br>
And Also I would like to know if in the grompp file I have to modify <br>
other parameters (I use a beredensed coupling) <br>
<br>
Thanks in advance <br>
Sorry for bothering you <br>
Best Regards <br>
Elena della Valle <br>
<br>
-- <br>
Elena della Valle <br>
Ph.D. Student in Electronic Engineering <br>
<br>
Department of Information Engineering, Electronics and Telecommunications <br>
Sapienza, University of Rome <br>
via Eudossiana, 18 00184 Rome <br>
<br>
<br>
<o:p></o:p></p>
</blockquote>
<p class="MsoNormal">Just a quick question: which version did you use? All development should be in the master version and this looks like uses something older.
<br>
<br>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology <br>
Dept. of Cell & Molec. Biol., Uppsala University. <br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. <br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se">
http://folding.bmc.uu.se</a> <br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Elena della Valle<o:p></o:p></pre>
<pre>Ph.D. Student in Electronic Engineering<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Department of Information Engineering, Electronics and Telecommunications<o:p></o:p></pre>
<pre>Sapienza, University of Rome<o:p></o:p></pre>
<pre>via Eudossiana, 18 00184 Rome<o:p></o:p></pre>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Elena della Valle<o:p></o:p></pre>
<pre>Ph.D. Student in Electronic Engineering<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Department of Information Engineering, Electronics and Telecommunications<o:p></o:p></pre>
<pre>Sapienza, University of Rome<o:p></o:p></pre>
<pre>via Eudossiana, 18 00184 Rome<o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Elena della Valle<o:p></o:p></pre>
<pre>Ph.D. Student in Electronic Engineering<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Department of Information Engineering, Electronics and Telecommunications<o:p></o:p></pre>
<pre>Sapienza, University of Rome<o:p></o:p></pre>
<pre>via Eudossiana, 18 00184 Rome<o:p></o:p></pre>
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