[gmx-users] HYP GROMOS
Hello, I have done calculations using standard GROMOS 43a1 and 53a6 parameters (GROMACS 3.3.3) for a 4-hydroxy-L-proline derivative (HYP), where the gamma-OH and the alpha-CO groups are trans to each other in the starting structure. However, over the course of MD the trans-configuration of these two substituents changes into a cis-configuration, which was not supposed to happen. Is there any way to avoid such isomerisation? Abil _ X Factor: latest video, features and more. Click here! http://clk.atdmt.com/GBL/go/115454063/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] How can I generate a Input *.gro file of coarse grain model?
Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use genbox editconf et al to generate the input *.gro files. For example, I can use genbox -cs -box 10 10 10 -o waterbox.gro to generate pure water box. But if I only have the files downloaded from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html; , and I use a *.top file which contains: #include martini_v2.0.itp #include martini_v2.0_lipids.itp [ system ] DPPC BILAYER [ molecules ] DPPC 128 W 2000 Can I generate a *.gro file according to this topology file using Gromacs' tools? If can, how do it? Appreciate any help in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] How can I generate a Input *.gro file of coarse grain model?
Hi Xuji, You'll have to have a coordinate file to start with, just like with your atomistic scale stuff. Whether this would be .pdb or .gro doesn't matter. If you have don't have coordinates, parameters are pretty useless. Maybe the Groningen guys are willingg to share you a .pdb file to play with. (Maybe the Groningen guys could write a comprehensive tutorial for the Martini stuff, to be linked on the wiki...). Cheers, Tsjerk On Sun, Oct 19, 2008 at 10:47 AM, xuji [EMAIL PROTECTED] wrote: Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use genbox editconf et al to generate the input *.gro files. For example, I can use genbox -cs -box 10 10 10 -o waterbox.gro to generate pure water box. But if I only have the files downloaded from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html; , and I use a *.top file which contains: #include martini_v2.0.itp #include martini_v2.0_lipids.itp [ system ] DPPC BILAYER [ molecules ] DPPC 128 W 2000 Can I generate a *.gro file according to this topology file using Gromacs' tools? If can, how do it? Appreciate any help in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] How can I generate a Input *.gro file of coarse grain model?
There are scripts provided on the MARTINI site to generate the necessary structure files, and the topology, IIRC. -Justin xuji wrote: Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use genbox editconf et al to generate the input *.gro files. For example, I can use genbox -cs -box 10 10 10 -o waterbox.gro to generate pure water box. But if I only have the files downloaded from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html; , and I use a *.top file which contains: #include martini_v2.0.itp #include martini_v2.0_lipids.itp [ system ] DPPC BILAYER [ molecules ] DPPC 128 W 2000 Can I generate a *.gro file according to this topology file using Gromacs' tools? If can, how do it? Appreciate any help in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] coulombic
Hi all users, I just got confused about whether I need to input the values of the coulombic interaction in the nb.itp file .If not, I wonder how the gromacs will recognize the coulombic interaction ,in the mdp.file? Sorry for this dull question. Thank you in advance. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] How can I generate a Input *.gro file of coarse grain model?
Hi , I was also engaged in dealing with the problem about the course grain model . I find that in this CG force field , the potential functions almost don't correspond to that in the gromacs. Hence, I wonder whether you know to how to define these new potential functions. Thank you in advance. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of xuji [EMAIL PROTECTED] Sent: Sunday, October 19, 2008 1:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] How can I generate a Input *.gro file of coarse grain model? Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use genbox editconf et al to generate the input *.gro files. For example, I can use genbox -cs -box 10 10 10 -o waterbox.gro to generate pure water box. But if I only have the files downloaded from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html; , and I use a *.top file which contains: #include martini_v2.0.itp #include martini_v2.0_lipids.itp [ system ] DPPC BILAYER [ molecules ] DPPC 128 W 2000 Can I generate a *.gro file according to this topology file using Gromacs' tools? If can, how do it? Appreciate any help in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Support of Saddle Point Calculations
Hello, I am fairly new to GROMACS but I have spent time running tutorials for several other molecular dynamics applications. I would like to know if the current framework for GROMACS has support for methods that calculate saddle point energy in first-order reactions. If so, are there examples I can read about? Jack ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Support of Saddle Point Calculations
Jack Shultz wrote: Hello, I am fairly new to GROMACS but I have spent time running tutorials for several other molecular dynamics applications. I would like to know if the current framework for GROMACS has support for methods that calculate saddle point energy in first-order reactions. If so, are there examples I can read about? First, GROMACS does not support reactions, unless you use the QM/MM methods in which case you have to look into e.g. Gaussian's way of doing a Transition State optimization. Second, you can do normal mode analysis which would give you indirectly the needed information, if you have a conformation that you know is the transition state. Jack ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 search the archive at http://www.gromacs.org/search before posting! 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] How can I generate a Input *.gro file of coarse grain model?
Hi xuji, I do not believe the scripts provided on the site deal with water. That is, unfortunately, you cannot take and equilibrated atomistic system and convert directly to the CG representation. What you will have to do is go to the test/model system page and download the pure water system. You can then use this as an input to genbox program. Cheers Mitch Quoting Justin A. Lemkul [EMAIL PROTECTED]: There are scripts provided on the MARTINI site to generate the necessary structure files, and the topology, IIRC. -Justin xuji wrote: Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use genbox editconf et al to generate the input *.gro files. For example, I can use genbox -cs -box 10 10 10 -o waterbox.gro to generate pure water box. But if I only have the files downloaded from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html; , and I use a *.top file which contains: #include martini_v2.0.itp #include martini_v2.0_lipids.itp [ system ] DPPC BILAYER [ molecules ] DPPC 128 W 2000 Can I generate a *.gro file according to this topology file using Gromacs' tools? If can, how do it? Appreciate any help in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
