Hello again,<br><br>As you mentioned, it makes sense that the starting umbrella potential a in the equation U = (1/2)K(x-a)^2 should be given in the .tpr file. I have looked over the manual and online though, and I still cannot see what portion of the pull code allows me to define the a. It seems that maybe GROMACS just takes the starting distance between the two atoms, and centers the umbrella potential around that distance? For instance, my starting configuration starts with the reference group and pull group 0.28 nm away. I have turned on the pull code in the .tpr file in order to do an umbrella sample and it looks like this:<br>
<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = Y Y Y<br>pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = Na+<br>pull_group1 = I-<br>pull_rate1 = 0.00<br>pull_k1 = 5000<br><br>I don't see how any of these designate where the bottom of the umbrella potential well lies (except for maybe pull_start - perhaps setting it to yes puts centers the umbrella potential on the COM of the system). So instead, maybe GROMACS realizes that Na+ and I- start 0.28 nm away, and uses this value as the center of the umbrella potential. <br>
<br>Is this the case? Or do one of these pull code designations dictate a?<br><br>Thanks,<br>Jennifer<br><br><div class="gmail_quote">On Fri, Apr 16, 2010 at 4:20 AM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se">jochen@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">Jennifer Casey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this?<br>
</blockquote></div>
Hi Jennifer!<br>
<br>
As pointed out by Chris, you can use provide the pull positions (g_wham -ix) OR the pull forces with -if. When giving the pullf files, g_wham simply computes the pull positions from the forces and calculates the histograms etc...<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Also, when using the pull code, I am allowed to define the spring constant K for umbrella sampling, but I do not designate where the umbrella potential is centered. How does gromacs determine this?<br>
</blockquote></div>
Umbrella positions and force constants (and pull geometry) are taken from the tpr files. That's why they must be provided to g_wham.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I am interested as I would like to create a PMF using umbrella integration (from code I will write myself) rather than use WHAM. To do this and still use the umbrella sampling runs used with GROMACS, I need to know where my umbrella potentials are centered.<br>
</blockquote></div>
If you want to integrate the mean forces, I would not use pull=umbrella but pull=constraint. You should get the same PMF compared to umbrella sampling and using g_wham.<br>
<br>
Please let me know if g_wham makes any trouble.<br>
<br>
Cheers,<br>
<br>
Jochen<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thank you,<br>
Jennifer<br>
</blockquote>
<br>
<br>
-- <br>
---------------------------------------------------<br>
Dr. Jochen Hub<br>
Molecular Biophysics group<br>
Dept. of Cell & Molecular Biology<br>
Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>
Phone: +46-18-4714451 Fax: +46-18-511755<br>
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