On Wed, Nov 19, 2008 at 10:20 AM, <[EMAIL PROTECTED]> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: RE: [gmx-users] sedoheptulose (Bernhard Knapp) > 2. Re: sedoheptulose (Mark Abraham) > 3. large charge group (Sunjoo Lee) > 4. RE: large charge group (Berk Hess) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Nov 2008 16:52:22 +0100 > From: Bernhard Knapp <[EMAIL PROTECTED]> > Subject: Re: RE: [gmx-users] sedoheptulose > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" > > thanks for the hints but unfortunately i still can not get the molecule > running. i tried with both prodrg server and x2top but with limited success: > > in the first case i generate the gro.pdb and .top file via the > webinterface [1] of prodrg by pasting my coordinate file into the > textbox. then i run the following commands: > > editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic -d 2.0 > genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o > sedoheptulose.water.pdb -p sedoheptulose.top -nice 0 > grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top > -o sedoheptulose.em.tpr > > but in the grompp commands the following error occurs: > > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: topio.c, line: 388 > > Fatal error: > Invalid order for directive moleculetype, file ""sedoheptulose.top"", > line 17 > ------------------------------------------------------- > > but in line 17 only "[ moleculetype ]" is written? > > > > in the second case I do not really understand the error message: > > x2top -f sedoheptulose.pdb -o sedoheptulose.top > > leads to: > > ------------------------------------------------------- > Program x2top, VERSION 3.3.1 > Source code file: futil.c, line: 537 > > Fatal error: > Library file ffG43a1.n2t not found in current dir nor in default > directories. > (You can set the directories to search with the GMXLIB path variable) > ------------------------------------------------------- > > > also in the faq i could not find a real guide how to simulate such a > molecule ... > > > > Bernhard > > > > > [1] http://davapc1.bioch.dundee.ac.uk/prodrg/index.html > > > > [EMAIL PROTECTED] wrote: > >>Message: 1 >>Date: Wed, 19 Nov 2008 13:25:07 +0000 >>From: "Kukol, Andreas" <[EMAIL PROTECTED]> >>Subject: RE: [gmx-users] sedoheptulose >>To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>Message-ID: >> <[EMAIL PROTECTED]> >>Content-Type: text/plain; charset="iso-8859-1" >> >>Yes, it is possible by deveoping your own topology. Pdb2gmx is not suitable >>for that purpose. >> >>It would be helpful to check out the documentation resources and manual, e.g. >> >>http://wiki.gromacs.org/index.php/FAQs >> >>x2top and the prodgr web-server might be some good starting points. >> >>Andreas >> >> >> >>From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Knapp >>Sent: 19 November 2008 12:54 >>To: gmx-users@gromacs.org >>Subject: [gmx-users] sedoheptulose >> >>Dear users >> >>I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via >>Gromacs. But already during pdb2gmx it comes up with: >>"Residue 'UNK' not found in residue topology database" which is obviously >>clear since sedoheptulose is not an amino acid. Is it somehow possible to >>simulate this molecule? >> >>the sedoheptulose data to start from is: >>ATOM 1 C UNK 0 -3.442 2.742 0.000 0.00 0.00 >>C+0 >>ATOM 2 C UNK 0 -2.108 3.512 0.000 0.00 0.00 >>C+0 >>ATOM 3 C UNK 0 -0.774 2.742 0.000 0.00 0.00 >>C+0 >>ATOM 4 C UNK 0 0.559 3.512 0.000 0.00 0.00 >>C+0 >>ATOM 5 C UNK 0 1.893 2.742 0.000 0.00 0.00 >>C+0 >>ATOM 6 C UNK 0 3.227 3.512 0.000 0.00 0.00 >>C+0 >>ATOM 7 O UNK 0 -0.774 1.202 0.000 0.00 0.00 >>O+0 >>ATOM 8 O UNK 0 0.559 5.052 0.000 0.00 0.00 >>O+0 >>ATOM 9 O UNK 0 1.893 1.202 0.000 0.00 0.00 >>O+0 >>ATOM 10 O UNK 0 -4.775 3.512 0.000 0.00 0.00 >>O+0 >>ATOM 11 O UNK 0 -2.108 5.052 0.000 0.00 0.00 >>O+0 >>ATOM 12 H UNK 0 -6.109 2.742 0.000 0.00 0.00 >>H+0 >>ATOM 13 H UNK 0 -0.774 5.822 0.000 0.00 0.00 >>H+0 >>ATOM 14 H UNK 0 1.893 5.822 0.000 0.00 0.00 >>H+0 >>ATOM 15 H UNK 0 0.559 0.432 0.000 0.00 0.00 >>H+0 >>ATOM 16 H UNK 0 3.227 0.432 0.000 0.00 0.00 >>H+0 >>ATOM 17 C UNK 0 4.560 2.742 0.000 0.00 0.00 >>C+0 >>ATOM 18 O UNK 0 5.894 3.512 0.000 0.00 0.00 >>O+0 >>ATOM 19 H UNK 0 7.228 2.742 0.000 0.00 0.00 >>H+0 >>ATOM 20 O UNK 0 3.227 5.052 0.000 0.00 0.00 >>O+0 >> >>cheers >>bernhard >> >> >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20081119/2faac396/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 20 Nov 2008 03:04:29 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] sedoheptulose > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Bernhard Knapp wrote: >> thanks for the hints but unfortunately i still can not get the molecule >> running. i tried with both prodrg server and x2top but with limited success: >> >> in the first case i generate the gro.pdb and .top file via the >> webinterface [1] of prodrg by pasting my coordinate file into the >> textbox. then i run the following commands: >> >> editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic -d 2.0 >> genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o >> sedoheptulose.water.pdb -p sedoheptulose.top -nice 0 >> grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top >> -o sedoheptulose.em.tpr >> >> but in the grompp commands the following error occurs: >> >> ------------------------------------------------------- >> Program grompp, VERSION 3.3.1 >> Source code file: topio.c, line: 388 >> >> Fatal error: >> Invalid order for directive moleculetype, file ""sedoheptulose.top"", >> line 17 >> ------------------------------------------------------- >> >> but in line 17 only "[ moleculetype ]" is written? > > This error really means what it says - this directive is given at a time > when it is not valid. You'll need to understand the .top file format, > which is explained with an example in section 5.7 of the manual. It > sounds like you should try out some tutorial material to get a handle on > some of the GROMACS ways of doing things. > >> also in the faq i could not find a real guide how to simulate such a >> molecule ... > > Developing a topology for a "new" molecule is not a good starting place > for a near-beginner with any MD package. You will need to read relevant > parts of the manual thoroughly. > > Mark > > > ------------------------------ > > Message: 3 > Date: Wed, 19 Nov 2008 10:01:01 -0600 > From: "Sunjoo Lee" <[EMAIL PROTECTED]> > Subject: [gmx-users] large charge group > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello All > > Recently I have figured out the biggest problem that made my system unstable. > I have parameterized a molecule pretty similar to octane. A single > charge group used to be assigned to this molecule. With 1 nm cut-off > distance for LJ interaction and the direct space for electrostatic > interaction, the system underwent severe volume fluctuation and at the > end crashed due to enormously large short range coulomb interaction > energy. The problem was temporarily resolved by using greater cut-off > distance such as 1.4 nm. But this fixation was not perfect when I put > this molecule into more complex system. Regardless of the cut-off > distance even to 1.8 nm did not solve the problem. The simulation > always terminated due to large coulomb energy even though no direct > contact or any weird structure was observed at that snapshot. > > With the help of many experts, I have made a single charge group into > three smaller charge group, which magically fixed all the problem that > I have had for almost 2 years. I know that charge group is only used > for neighbor search. Can anybody tell me how the size of charge group > can influence the interaction between atoms depending on the > complexity of the system and cut-off distance?? > > Thank you in advance > > Sunjoo > > > ------------------------------
Hello Berk Thank you for the clear explanation. It makes very good sense what was the problem! Thank you Sunjoo > > Message: 4 > Date: Wed, 19 Nov 2008 17:15:24 +0100 > From: Berk Hess <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] large charge group > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > The charge groups "only" affect the neighbor searching, > which in practice means they affect everything. > > In Gromacs atoms in two different charge groups will only interactions > when the center of geometry of the two charge groups is within rlist. > > The worst case scenario, which has happend to several people, is: > A molecule with a radius of about 0.5 nm is one charge group. > If the cut-off is 1 nm, two molecules will only really start interacting > when they already overlap. > > In 4.0 I put a check on large charge groups. > If you have charge groups of more than 10 atoms, grompp will now > warn you with: > "The largest charge group contains %d atoms.\n" > "Since atoms only see each other when the centers of geometry of the charge > groups they belong to are within the cut-off distance, too large charge > groups can lead to serious cut-off artifacts.\n" > "For efficiency and accuracy, charge group should consist of a few atoms.\n" > "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.\n", > > Berk > >> Date: Wed, 19 Nov 2008 10:01:01 -0600 >> From: [EMAIL PROTECTED] >> To: gmx-users@gromacs.org >> Subject: [gmx-users] large charge group >> >> Hello All >> >> Recently I have figured out the biggest problem that made my system unstable. >> I have parameterized a molecule pretty similar to octane. A single >> charge group used to be assigned to this molecule. With 1 nm cut-off >> distance for LJ interaction and the direct space for electrostatic >> interaction, the system underwent severe volume fluctuation and at the >> end crashed due to enormously large short range coulomb interaction >> energy. The problem was temporarily resolved by using greater cut-off >> distance such as 1.4 nm. But this fixation was not perfect when I put >> this molecule into more complex system. Regardless of the cut-off >> distance even to 1.8 nm did not solve the problem. The simulation >> always terminated due to large coulomb energy even though no direct >> contact or any weird structure was observed at that snapshot. >> >> With the help of many experts, I have made a single charge group into >> three smaller charge group, which magically fixed all the problem that >> I have had for almost 2 years. I know that charge group is only used >> for neighbor search. Can anybody tell me how the size of charge group >> can influence the interaction between atoms depending on the >> complexity of the system and cut-off distance?? >> >> Thank you in advance >> >> Sunjoo >> _______________________________________________ >> gmx-users mailing list gmx-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 > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20081119/67b68058/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 55, Issue 106 > ****************************************** > _______________________________________________ gmx-users mailing list gmx-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
