Re: Re: [gmx-users] Atomic distances problems using gmxcheck
Hello David: Yes, you are right. the value equals to the square of the distance, approximately. In fact, the force field I used was GROMOS96 43a1 force field. I have also tried the other kind of force fields, such as OPLS-AA/L all-atom force field, the same warning was reported, but the "should be" value seemed much more reasonable. Thank you very much for your help! 在 2007-09-19三的 08:24 [EMAIL PROTECTED] > Message: 5 > Date: Wed, 19 Sep 2007 08:24:25 +0200 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Atomic distances problems using gmxcheck > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > yudaqi wrote: > > Hello gmx-users: > > When using gmxcheck to compare the bond length in .tpr files and .trr > > files, I get the following long list error: > > Distance between atoms 1 and 2 is 0.100, should be 0.010 > > Distance between atoms 1 and 3 is 0.101, should be 0.010 > > Distance between atoms 1 and 4 is 0.100, should be 0.010 > > Distance between atoms 1 and 5 is 0.146, should be 0.022 > > If you look close the expected distance seems to be the square of the > distance. Could it be you are using a GROMOS force field? > > > .. > > I have searched the maillists in the web site of gromacs, and found the > > same problems has been issued by other users. However, I can not find > > detailed explanations about this. > > So I wonder why the bond length should be of the order of 0.01 nm? > > Thank you very much. > > YuDaqi > > > > ___ > > 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
Re: [gmx-users] Atomic distances problems using gmxcheck
yudaqi wrote: Hello gmx-users: When using gmxcheck to compare the bond length in .tpr files and .trr files, I get the following long list error: Distance between atoms 1 and 2 is 0.100, should be 0.010 Distance between atoms 1 and 3 is 0.101, should be 0.010 Distance between atoms 1 and 4 is 0.100, should be 0.010 Distance between atoms 1 and 5 is 0.146, should be 0.022 .. I have searched the maillists in the web site of gromacs, and found the same problems has been issued by other users. However, I can not find detailed explanations about this. So I wonder why the bond length should be of the order of 0.01 nm? I fixed it in CVS. Will be in 3.3.2 Thank you very much. YuDaqi ___ 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. 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] Atomic distances problems using gmxcheck
yudaqi wrote: Hello gmx-users: When using gmxcheck to compare the bond length in .tpr files and .trr files, I get the following long list error: Distance between atoms 1 and 2 is 0.100, should be 0.010 Distance between atoms 1 and 3 is 0.101, should be 0.010 Distance between atoms 1 and 4 is 0.100, should be 0.010 Distance between atoms 1 and 5 is 0.146, should be 0.022 If you look close the expected distance seems to be the square of the distance. Could it be you are using a GROMOS force field? .. I have searched the maillists in the web site of gromacs, and found the same problems has been issued by other users. However, I can not find detailed explanations about this. So I wonder why the bond length should be of the order of 0.01 nm? Thank you very much. YuDaqi ___ 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. 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
