If I solvate my GPCR into the DPPC128 system using genbox, there are only about 50 lipids left, which I think are too few, so I want a larger starting structure.<br><br>According to your note, when I did step 3, loaded my DPPC183 system to VMD, I found the edges lined up poorly, there is are gaps between two periodic cells. I also try other system like DPPC200, DPPC150, but only the original dppc128 system, I've equilibrated it for 2ns, have no gap between two periodic cells.
<br><br>So, I will try another starting structure, like POPC, DMPC or your POPE. But I still can't figure out why there are gaps when using genbox to extend the DPPC system.<br><br><div><span class="gmail_quote">On 9/9/06,
<b class="gmail_sendername"><a href="mailto:chris.neale@utoronto.ca" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
chris.neale@utoronto.ca</a></b> <<a href="mailto:chris.neale@utoronto.ca" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">chris.neale@utoronto.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
>According to your suggestion, I did a energy minimization and then a MDS<br>>with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were<br>>simulated with no constraint. This time I use semiisotropic pressure
<br>>coupling with tau_p=5. The system will be equilibrated with water<br>>constrained for 1ns, do you think it's enough?<br><br>It will be more than enough. Use vmd to watch the trajectory. It's important<br>actually look at the structures.
<br><br>>The reason why I want to extend the system is because that I've got a GPCR,<br>>and I want to simulate it in a DPPC membrane environment, but the z<br>>dimension of the membrane, downloaded from Dr. Tielman's websit, was not
<br>>large enough, when I align the protein to the z axis of the membrane I find<br>>the two ends of the protein are poking out of both water layers.<br><br>In this case you may not need to extend the lipid. Why not just use editconf to
<br>increase the z dimension while keeping the x and y constant. Then insert your<br>protein, re-solvate, re-equilibrate, and your into production. If your lipid<br>takes up a maximum amout of space D in the xy-plane, then x and y need only be
<br>equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra amount<br>in case the protein fluctuations make it larger during the simulation].<br><br>>Back to the previous question, after solvate the lipids in water, can I
<br>>remove the water placed in the membrane with excel instead of script? Cause<br>>with editconf we can know the z dimension of the lipids_only system, let's<br>>say 6, so if I center the whole system with 0 0 0, the water molecules with
<br>>z coordinates below 3 and above -3 will be excluded. If I'm right, I think<br>>excel can do it too, or the scripts have some advantages?<br><br>Sure you can use excel, but I am not sure how that is going to affect your
<br>formatting or how gromacs responds to formatting (i.e. spaces / tabs / the<br>number of each) So scrips have 2 advantages: 1)formatting is easily maintained,<br>2)if you need to do it a second time you just type one command. After using
<br>excel (or a script) make sure to update you topology file to indicate the number<br>of waters.<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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