<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Thank you so much for your help , my pdb file says that gen_seed = 473529 so i will change it to different numbers , but i saw online that some </span><span> gen_seed = -1 and that to generate random seed is that correct ??</span></div><div><span> also please how i can control the starting initial states so that i can have starting from more one initial states?? tried looking it up on line but did not find that much information.<br></span></div><div> <br><span></span></div><div><span>Thank you so much <br></span></div><div><br><span></span></div><div><span>fatima ezahra <br></span><style type="text/css">pre.cjk { font-family: "DejaVu Sans",monospace; }p { margin-bottom: 0.08in; }</style>
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</div><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight: bold;">De :</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">À :</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Envoyé le :</span></b> Jeudi 7 Juillet 2011 15h55<br><b><span style="font-weight: bold;">Objet :</span></b> Re: Re : Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of peptides<br></font><br><br><br>errabah fatima ezzahra wrote:<br>> I am sorry to be asking you again but do you start with different velocities by changing the temperature that will lead to change in velocities, i ma new to Gromacs so i dont know where to change he velocities, i
checked the mdp file and i didn't see any velocity<br>> <br><br>Keep the temperature the same and change gen_seed.<br><br>-Justin<br><br>> thank you<br>> <br>> Fatima ezzahra<br>> <br>> ------------------------------------------------------------------------<br>> *De :* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *À :* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Envoyé le :* Jeudi 7 Juillet 2011 14h55<br>> *Objet :* Re: Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of peptides<br>> <br>> <br>> <br>> errabah fatima ezzahra wrote:<br>> > *<br>> ><br>> > hello<br>> > Does anybody knows why The N and C termini of peptides can be neutralized before running simulation
of peptides ?? i read this some where in a research paper , they dont say why but they do that using acetyl amine groops. Probably to evoid the repulsive interactions between the end of the peptides , please correct if i am wrong as my chemistry is not good, my one trimer is made of 3 peptides that ends with GLU LEU LEU and the other trimer ends with is LEU GLU LEU , should i worry about neutralizing the c and N termini<br>> ><br>> <br>> Capping groups can be added to termini using different software programs. There is no utility in Gromacs to do so. Once built, choose 'None' for the termini when running pdb2gmx to build a normal peptide bond between the terminal residue(s) and capping group(s).<br>> <br>> Such groups are often added (1) if artificial terminal attraction or repulsion should be avoided or (2) if the modeled peptide is a segment of a longer polypeptide or protein, in which case such integral
charges are an incorrect representation of reality.<br>> <br>> > Also what the important of running 20 simulations of the same 6 peptides ???. is that to compare the 20 simulation results and see **** which give better simulation sorry if my question are something i should know. i am trying to find how to get six peptides to self assemble to a hexamer . i will really appreciate your answers.<br>> ><br>> <br>> Running multiple simulations of a given configuration (using different starting velocities) gives better sampling. You can't conclude anything from a single trajectory. Just as you wouldn't run a single experiment on the bench and call it conclusive, so too is it true of simulations - if you run just one simulation, how do you know you're not seeing the one outlier in the data set?<br>> <br>> -Justin<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]vt.edu | (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>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> <br>> <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]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
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