Re: [gmx-users] Why should I repeat my simulation?
On 5 Oct 2014 04:18, Justin Lemkul jalem...@vt.edu wrote: On 10/4/14 5:15 PM, fatemeh ramezani wrote: Dear gmx-users I performed a MD simulation with gromacs software and after sending my results to a journal, referee said Simulations needs to be repeated with different initial velocity (seed) to make sure that the results are not simulation artifacts.It is needed to ensure that the simulation represents true dynamics of the system. It is really need to I repeat my simulation (that is very time-consuming process) or you can help me to providea compelling reason for not repeating. The reviewer is right. A single simulation is generally insufficient to provide convincing evidence of any behavior, unless it is exceptionally long and shows, for instance, reversible behavior. In reality, no simulation is probably ever truly converged. That is why it is standard practice to conduct multiple simulations, exactly as the reviewer says. One would never perform a single biological assay and claim it to be exactly correct, why should one simulation be the exact answer? Perhaps your one simulation would end up being the outlier in a data set. -Justin Agree with Justin. At least three replicas should be done. Note also that comparing different simulations can tell you more interesting things about your system. It's always not only necessary but enriching. M. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why should I repeat my simulation?
Some care must be taken with the use of the term replica, due to the amount of replica-exchange schemes around. The replicate simulations being talked about here do not imply exchange schemes and different hamiltonians. Just to make things clearer. João On Sun, Oct 5, 2014 at 4:15 PM, massimo sandal deviceran...@gmail.com wrote: On 5 Oct 2014 04:18, Justin Lemkul jalem...@vt.edu wrote: On 10/4/14 5:15 PM, fatemeh ramezani wrote: Dear gmx-users I performed a MD simulation with gromacs software and after sending my results to a journal, referee said Simulations needs to be repeated with different initial velocity (seed) to make sure that the results are not simulation artifacts.It is needed to ensure that the simulation represents true dynamics of the system. It is really need to I repeat my simulation (that is very time-consuming process) or you can help me to providea compelling reason for not repeating. The reviewer is right. A single simulation is generally insufficient to provide convincing evidence of any behavior, unless it is exceptionally long and shows, for instance, reversible behavior. In reality, no simulation is probably ever truly converged. That is why it is standard practice to conduct multiple simulations, exactly as the reviewer says. One would never perform a single biological assay and claim it to be exactly correct, why should one simulation be the exact answer? Perhaps your one simulation would end up being the outlier in a data set. -Justin Agree with Justin. At least three replicas should be done. Note also that comparing different simulations can tell you more interesting things about your system. It's always not only necessary but enriching. M. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] constraint and restraints
Dear GROMACS users, Is it possible with Gromacs and how could be done a simulation keeping almost all protein residues fixed except for instance resi 361-372 ? Will the extraction of resulting rmsd for each residue give some knowledge regarding its flexibility (mobility) ? Regards, N.S. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] constraint and restraints
Hi Niyaz, You can set position restraints for all atoms not in that residue range. Whether it makes sense is another question. The dynamics is usually coupled throughout the protein. Cheers, Tsjerk On Sun, Oct 5, 2014 at 10:03 PM, niyaz.sabir niyaz.sa...@gmail.com wrote: Dear GROMACS users, Is it possible with Gromacs and how could be done a simulation keeping almost all protein residues fixed except for instance resi 361-372 ? Will the extraction of resulting rmsd for each residue give some knowledge regarding its flexibility (mobility) ? Regards, N.S. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Invalid order for directive bondtypes
Dear gromacs users I want to do MD simulation of a CNT. I used aromatic carbon from charmm.ff I created a cnt.ff folder containing following files: ffcnt.atp: --- CA12.01100 ;aromatic C - ffcnt.n2t: --- CCA0.00 12.0113C 0.141 C 0.141 C 0.141 CCA0.00 12.0112C 0.141 C 0.141 - ffcntbonded.itp: [ bondtypes ] ; i j func b0 kb CA CA10.1375 0.0 [ angletypes ] ; i j k func th0 cth ub0 cub CA CA CA 5 120.00 0.0 0.24162 29288.0 [ dihedraltypes ] ; i j k l funcphi0cp mult CA CA CA CA 9 180.00 0.0 2 - ffcntnonbonded.itp: - [ atomtypes ] ;nameat.nummasschargeptypesigma epsi CA 612.011000.00A 0.335 0.234463 - ffcnt.rtp: -- [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 5 921 3 1 0 [ ALA ] [ atoms ] NNH1-0.47 0 HNH0.31 1 CACT10.07 2 HAHB0.09 3 CBCT3-0.27 4 HB1HA0.09 5 HB2HA0.09 6 HB3HA0.09 7 CC0.51 8 OO-0.51 9 . . . - forcefield.itp: #define _FF_CNT [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 1 2 yes 1.01.0 #include ffcntbonded.itp #include ffcntnonbonded.itp - After creating cnt.top file using g_x2top, I used grompp for energy minimization, but I encountered with Fatal Error: Syntax error - File ffcntbonded.itp, line 1 Last line read: '[ bondtypes ]' Invalid order for directive bondtypes Before doing MD simulation, I checked carbon nanotube in the GROMACS website: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=nanotube In my opinion, my manner is true. How to solve this problem? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
