Re: [gmx-users] The molecule size
Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96aUsually a garbage result as output means that you had either garbage asinput, or garbage for the algorithm. Find a published article thatdescribes a similar simulation and adapt their method suitably.Otherwise describe your method more thoroughly (e.g. how large was thebox, what ensemble did you use, equilibration regime, etc.) and maybesomeone has some judgement they can share with you.Mark Hi Mark: Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details. The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl= no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time is about 1ns. So i think the system has been relaxed enough. Is there any error in my process? Maybe the residue parameter for PVME is also needed for discuss. They are: [ VME ] [ atoms ] ; atom type charge cgnr CN Gasteiger CAB CH1 0.142 1 ; CN CAA CH2 0.035 1 ; CN OAD OE -0.352 1 ; CN CAC CH3 0.174 1 ; CN [ bonds ] ; ai aj fu CAA CAB gb_27 CAB OAD gb_53 CAC OAD gb_53 CAB +CAA gb_27 [ angles ] ; ai aj ak fu c0, c1, ... CAA CAB OAD ga_30 CAB OAD CAC ga_10 OAD CAB +CAA ga_30 CAA CAB +CAA ga_15 CAB +CAA +CAB ga_15 [ dihedrals ]; ai aj ak al fu c0, c1, m, ... CAA CAB OAD CAC gd_13 CAA CAB +CAA +CAB gd_34+CAA CAB OAD CAC gd_13CAB +CAA +CAB +OAD gd_1 *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The molecule size
主月 ：） wrote: Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Two things, - maybe you need a larger systems - maybe g_gyrate does not take periodicity into account correctly. extract some single molecules and look at them in a viewer, or write your own script to compute Rg. - have you used pbc = full for the simulations? Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark *Hi Mark:* *Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details.* ** *The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl = no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time is about 1ns. So i think the system has been relaxed enough.* ** *Is there any error in my process?* ** *Maybe the residue parameter for PVME is also needed for discuss. They are:* ** -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The molecule size
Hi: Two meltmodels were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition. The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Thanks in advance. *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The molecule size
主月 ：） wrote: Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
