<div dir="ltr"><div>Thanks Justin,</div>
<div> </div>
<div>it seems to help, i have another general question that you might help me with:</div>
<div> </div>
<div>should i define the distances for the umbrella sampling run in some file and then run it?(i saw something about *.ppa file but couldn't find any further instructions in the mannual..)</div>
<div>will this file apply for the WHAM analysis after the run?</div>
<div> </div>
<div>thanks, </div>
<div>Amir<br><br></div>
<div class="gmail_quote">On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<div class="h5"><br><br>Amir Marcovitz wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br> my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one of them (SRP) and negatively charged on the other plate (SRN).<br>
i want to perform a simulation with umbrella sampling between the 2 so i defined the pulling section parameters in the .mdp parameter file as following:<br> ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force<br>
pull = umbrella<br>; Pull geometry: distance, direction, cylinder or position<br>pull_geometry = distance<br>; Select components for the pull vector. default: Y Y Y<br>pull_dim = Y Y Y<br>
; Cylinder radius for dynamic reaction force groups (nm)<br>pull_r1 = 1<br>; Switch from r1 to r0 in case of dynamic reaction force<br>pull_r0 = 1.5<br>pull_constr_tol = 1e-06<br>
pull_start = no<br>pull_nstxout = 10<br>pull_nstfout = 1<br>; Number of pull groups<br>pull_ngroups = 2<br>; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)<br>
pull_group0 = SRP<br>pull_weights0 = 1<br>pull_pbcatom0 = 0<br>pull_group1 = SRN<br>pull_weights1 = 1<br>pull_pbcatom1 = 0<br>pull_vec1 = 0.0 1.0 0.0<br>
pull_init1 = 1.5<br>pull_rate1 = 0<br>pull_k1 = 1<br>pull_kB1 = 0<br> when proccesing the file with grompp i get the following error:<br> *Fatal error:<br>Number of weights (1) for pull group 0 'SRP' does not match the number of atoms (36)*<br>
is someone recognizing my mistake?<br></blockquote><br></div></div>Please refer to the manual (<a href="http://manual.gromacs.org/" target="_blank">manual.gromacs.org</a> is quite handy), you will find:<br><br>"Optional relative weights which are multiplied with the masses of the atoms to give the total weight for the COM. The number should be 0, meaning all 1, or the number of atoms in the pull group."<br>
<br>I also think your value for pull_ngroup is wrong. It appears you are pulling SRN with respect to SRP, so you only have one pull group, not two.<br><font color="#888888"><br>-Justin<br><br></font>
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<div class="im">does someone has an experience with umbrella sampling in GROMACS?<br> thanks'<br>amir<br></div>*<br>*<br><br></blockquote>
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<div class="h5"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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