Hi Justin If I want to have Decane.itp file in Amber forcefield for TIP4P-EW what should I do?
Thanks Regards Maria On Sun, May 1, 2011 at 6:27 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: amber force field (lina) > 2. Re: amber force field (Justin A. Lemkul) > 3. Re: reg error in coordinate file (Justin A. Lemkul) > 4. Re: How to use Inflategro with different lipid types > (Justin A. Lemkul) > 5. Re: How to use Inflategro with different lipid types > (Thomas Piggot) > 6. Re: Fatal error: Attempting to read a checkpoint file of > version 12 with code of version 4 (Faezeh Kargar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 1 May 2011 19:23:12 +0800 > From: lina <lina.lastn...@gmail.com> > Subject: Re: [gmx-users] amber force field > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTinZev64g49iTq2Sm4wK2Pf=xfr...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > In latest version of gromacs (4.5.4 or earlier) > > The amber force fields were provided. > > > -- > Best Regards, > > lina > > > ------------------------------ > > Message: 2 > Date: Sun, 01 May 2011 08:59:35 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] amber force field > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dbd5937.1030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Maria Hamilton wrote: > > Hi all friends > > > > If I want to use tip4pew model for water from Amber forcefield, can I > > use itp files in PRODRG site for the other components? > > > > PRODRG topologies are (supposedly) compatible with Gromos force fields, but > TIP4P-EW is not implemented for any of these parameter sets. Any attempt > to > combine these would inevitably result in fatal errors from grompp about > missing > atomtypes. More to the point, one should never mix and match force fields. > See, for instance, the discussion at: > > http://www.gromacs.org/Documentation/How-tos/Parameterization > > -Justin > > > Thanks > > > > Regards > > > > Maria > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Sun, 01 May 2011 09:06:04 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] reg error in coordinate file > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dbd5abc.8050...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > vidhya sankar wrote: > > Dear gmx-user, > > when i run Equilibration Phase (nvt.mdp) i got > > the .gro files as follows > > that is co-ordinates not defined in my .gro file > > What should i change in my mdp file in order to remove 'nan' and to > > obtain coordinate? > > I doubt the problem is that simple. "Nan" means "not a number," and thus > represents some infinite value. So either: > > 1. your system blew up at the last step when the .gro file was written > 2. there is some bug that needs to be fixed > 3. your file system had some problem writing the .gro file > > To address (1), check the .log file for any pertinent messages about > instability. For (2), you'll have to at least provide your Gromacs > version, > input settings (.mdp file), and perhaps a description of the hardware. For > (3), > check your output trajectory with gmxcheck and/or watch it in VMD (or your > favorite viewer) and if its contents are normal and the .gro file is the > only > aberrant output, then it's your file system's fault, no Gromacs'. > > <snip> > > > 6.56000 4.36200 12.00000 > > For a system of just 80 atoms, this box seems extraordinarily large. Quite > likely your system blew up. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Sun, 01 May 2011 09:10:00 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] How to use Inflategro with different lipid > types > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dbd5ba8.9060...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Ioannis Beis wrote: > > Dear gromacs users, > > > > I am a new user of gromacs. I am currently trying to build a large > > bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and > > no protein embedded in it. I have used single lipids from > > pre-equilibrated bilayers available at Mr. Tieleman's website. The > > distance of center of mass of neighboring lipids is 1 nm, so there are > > small areas with overlaps. I was hoping that I would be able to inflate > > my membrane and have the lipids totally free of overlaps using > > Inflategro. Subsequently, I was planning to use the shrinking steps to > > bring the membrane into physiological size. Is this strategy valid in > > the first place? If not, I kindly ask for an alternative. > > > > In case this method can be used, despite "To identify the lipid species > > their actual residue name must be given" which is mentioned in the > > methodology, the form "INFLATEGRO bilayer.gro scaling_factor > > lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat > > (protein)" only allows the use of one lipid type. How is it possible to > > run perl with all lipid types at once? I have tried performing > > inflations using one lipid type at a time and they work. [It worths > > mentioning that the coordinates of the rest two (uninflated) lipid types > > slightly change without equilibration (I assume this has to do with > > Inflategro trying to force the molecules avoid overlaps)]. But I can't > > treat my membrane as a system that way. I have read the publication > > introducing the methodology, but it didn't help me solve my problem. > > > > I would be grateful if someone could help, also taking into account that > > I am > > inexperienced. > > > > If you want to use InflateGRO, then you'll have to modify the code to do > so. It > handles only one lipid type. > > The alternative is to use "normal" MD simulations to pack the membrane. On > such > approach (just thinking out loud here, so it may not work) might be to > simulate > your membrane (maybe without water) with some external pressure applied to > the > x-y plane to compress the lipids together. You may need position > restraints on, > i.e., the lipid headgroups in the z-dimension only during this procedure so > the > lipids do not simply slam into one another and distort the membrane. Once > you've achieved a reasonable membrane, solvate and equilibrate for a longer > period of time in the presence of solvent and absence of any restraints. > > -Justin > > > Kindest regards, > > Yiannis > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 5 > Date: Sun, 1 May 2011 14:41:09 +0100 > From: Thomas Piggot <t.pig...@soton.ac.uk> > Subject: Re: [gmx-users] How to use Inflategro with different lipid > types > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dbd62f5.9000...@soton.ac.uk> > Content-Type: text/plain; charset="UTF-8"; format=flowed > > Hi, > > To construct the bilayer I would just take an equilibrated POPC bilayer > and then randomly pick lipids to change to POPE (just by a simple > renaming of these lipids and the atom names in the headgroup) and DPPC > (which would just require deletion of two united-atoms from the sn-2 > chains and renaming of the lipids). Then just run for an equilibration > on the bilayer to allow the changes to take effect. > > There are other approaches you could take but I see this as the simplest > solution. > > Cheers > > Tom > > Justin A. Lemkul wrote: > > > > Ioannis Beis wrote: > >> Dear gromacs users, > >> > >> I am a new user of gromacs. I am currently trying to build a large > >> bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and > >> no protein embedded in it. I have used single lipids from > >> pre-equilibrated bilayers available at Mr. Tieleman's website. The > >> distance of center of mass of neighboring lipids is 1 nm, so there are > >> small areas with overlaps. I was hoping that I would be able to inflate > >> my membrane and have the lipids totally free of overlaps using > >> Inflategro. Subsequently, I was planning to use the shrinking steps to > >> bring the membrane into physiological size. Is this strategy valid in > >> the first place? If not, I kindly ask for an alternative. > >> > >> In case this method can be used, despite "To identify the lipid species > >> their actual residue name must be given" which is mentioned in the > >> methodology, the form "INFLATEGRO bilayer.gro scaling_factor > >> lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat > >> (protein)" only allows the use of one lipid type. How is it possible to > >> run perl with all lipid types at once? I have tried performing > >> inflations using one lipid type at a time and they work. [It worths > >> mentioning that the coordinates of the rest two (uninflated) lipid types > >> slightly change without equilibration (I assume this has to do with > >> Inflategro trying to force the molecules avoid overlaps)]. But I can't > >> treat my membrane as a system that way. I have read the publication > >> introducing the methodology, but it didn't help me solve my problem. > >> > >> I would be grateful if someone could help, also taking into account that > >> I am > >> inexperienced. > >> > > > > If you want to use InflateGRO, then you'll have to modify the code to do > so. It > > handles only one lipid type. > > > > The alternative is to use "normal" MD simulations to pack the membrane. > On such > > approach (just thinking out loud here, so it may not work) might be to > simulate > > your membrane (maybe without water) with some external pressure applied > to the > > x-y plane to compress the lipids together. You may need position > restraints on, > > i.e., the lipid headgroups in the z-dimension only during this procedure > so the > > lipids do not simply slam into one another and distort the membrane. > Once > > you've achieved a reasonable membrane, solvate and equilibrate for a > longer > > period of time in the presence of solvent and absence of any restraints. > > > > -Justin > > > >> Kindest regards, > >> Yiannis > >> > > > > -- > Dr Thomas Piggot > University of Southampton, UK. > > > ------------------------------ > > Message: 6 > Date: Sun, 1 May 2011 18:18:12 +0430 (IRDT) > From: "Faezeh Kargar" <f_kar...@iasbs.ac.ir> > Subject: Re: [gmx-users] Fatal error: Attempting to read a checkpoint > file of version 12 with code of version 4 > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: <28288.85.185.211.70.1304257692.squir...@mail.iasbs.ac.ir> > Content-Type: text/plain; charset="utf-8" > > > <html><div> > > > Thank you very > much for your reply. could you please tell me if there is any way to solve > this problem and restart running the code? > Karagr > > > > On 30/04/2011 11:37 PM, Faezeh Kargar wrote: > >> > >> > >> > On 4/30/2011 7:22 PM, Faezeh Kargar > wrote: > >> >> > >> >> Dear gmx users, > >> >> > >> >> My code stops running because > of electricity voltage oscillation. it > >> >> happened for > several times and each time I restarted running my code. > >> > >> but for this time with command > >> >> > >> >> mdrun -s topol.tpr -x > >> >> > traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt > >> >> -e > ener.part0002.part0003.part0004.part0004.part0005.edr -g > >> > >> md.part0002.part0003.part0004.part0004.part0005.log & > >> >> > >> >> I used this command before > without any error. but now I encountered > >> >> error like > this: > >> >> > >> >> > >> >> > Program mdrun, VERSION 4.0.7 > >> >> Source > >> > >> code file: checkpoint.c, line: 565 > >> >> > >> >> Fatal error: > >> >> Attempting > >> >> to read a checkpoint file of version 12 with code of > version 4 > >> >> > >> >> I looked at the > file "checkpoint.c". at first the version of > >> > >> checkpoint file is 4 but I do not know how and why it changes. > >> >> > >> > > >> > The usual reason > for this kind of error is that you're using an old > >> > > version of GROMACS to access a file written by a new version. That's > >> not > >> > a good idea. > >> > > >> > Mark > >> > > >> > >> Thank > you for your reply. I just use version 4.0.7 of GROMACS and all > >> of files are written by this version. as I said before, I > could > >> restart running of my codes with this command without > any problem. > >> > > > > Version 12 is that used in > 4.5.x, so I think you are using that version. > > Someone may have > changed the software and not told you about it (in > > which case, > tell them to stop wasting people's time). Or you've migrated > > > files from one place to another, or something similar. > > > > Mark > > -- > > gmx-users mailing list > gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please > search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > > This message has been scanned for viruses > and > > dangerous content by MailScanner, and is > > believed > to be clean. > > > > > > > -- > 83_kargar > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110501/e36122c4/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 85, Issue 2 > **************************************** >
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