<div>Dear David and Mauricio,</div>
<div> </div>
<div>I am also confused about the details of dgdl (or dHdl) calculation in GROMACS. For example, if the lambda is fixed at certain value, how did the program determine dHdl?</div>
<div>My initial understanding was kind of similiar to that of Mauricio that dHdl equals the difference in total potential energy between two time frame (snapshots). However, this seems does not make sense when lambda is fixed. Could you give more details about the calculation of the derivative dHdl at each snapshot? Thank you.
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<div>Best regards,</div>
<div> </div>
<div>Lei Zhou<br><br> </div>
<div><span class="gmail_quote">On 11/6/06, <b class="gmail_sendername">David Mobley</b> <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Mauricio,<br><br>I'm somewhat confused by your question and notation. However, I think<br>the basic answer is something like this: In molecular dynamics, you
<br>know the Hamiltonian from which you are sampling; call it H(x,p, l),<br>where x denotes all of the positions, p the momentums, and l lambda.<br>This, of course, is closely linked to the potential energy. Anyway, at<br>
any snapshot, you can simply take the derivative dH(x,p,l)/dl, and you<br>have dH/dl at that snapshot. This is usually straightforward since you<br>know the dependence of all of the terms in your Hamiltonian on lambda,<br>
so you actually have the functional form for dH/dl as well -- so it<br>just involves taking the appropriate combination of positions,<br>momentums, etc. This is of course all handled internally by the code.<br><dH/dl>, then, is just the time-average of dH/dl, which can be
<br>evaluated every step by the code.<br><br>I am not sure if that's helpful at all, as I'm not entirely sure what<br>problem you're having. After all, whenever you do TI calculations in<br>GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for every
<br>snapshot in an xvg output file. Are you just confused about how the<br>code gets this (I think I just answered that above), or are you trying<br>to figure out how to use it? If you're confused about how to use it,<br>
try to ask a question that relates to the specific issue you're<br>confused about.<br><br>Best wishes,<br>David Mobley<br>UCSF<br><br><br>On 11/5/06, Mauricio Sica <<a href="mailto:msica@unq.edu.ar">msica@unq.edu.ar</a>
> wrote:<br>> Dear experts<br>><br>> I am doing FEP (thermodynamic integration method) simulations.<br>> I have a questions about <dH/dl> calculation in GROMACS.<br>> Take in mind equation 3.77 from the GROMACS
3.3 manual.<br>> There, dA/dl is calculated as<br>><br>> dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = <dA/dl>NVT;l }<br>><br>> where SS are doble integrals (sorry for the notation).<br>><br>
> My question is: how is (dH/dl) (in the middel-term of the equation)<br>> calculated?<br>> My idea is that the difference V(L=1)-V(L=0) is calculated for every time<br>> step (irrespective of the lambda value of the simulation) and <dG/dl> is
<br>> the time average of that difference.<br>><br>> <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 ><br>><br>> Is this correct?<br>><br>><br>> Thanks<br>><br>><br>><br>> _______________________________________________
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