Message: 5 Date: Mon, 04 Nov 2013 13:32:52 -0500 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Analysis tools and triclinic boxes To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <5277e854.9000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Justin, Thanks for the response. My question was prompted by line 243 in gmx_cluster.c which states "/* Should use pbc_dx when analysing multiple molecueles,but the box is not stored for every frame.*/" I just wanted to verify that analysis tools are written for any box shape. Cheers, Stephanie On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote: > Dear all, > > I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail > list, it is my understanding that the default box shape in gromacs in a > triclinic box. Can I assume that all the analysis tools also work for a > triclinic box. > All analysis tools should work correctly for all box types. Is there a specific issue you are having, or just speculation? -Justin -- ============================== ==================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== On Mon, Nov 4, 2013 at 12:28 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: Re: Installation Gromacs 4.5.7 on rocluster cluster with > centos 6.0 (Mark Abraham) > 2. Analysis tools and triclinic boxes (Stephanie Teich-McGoldrick) > 3. Group protein not found in indexfile (Steve Seibold) > 4. Re: Group protein not found in indexfile (Justin Lemkul) > 5. Re: Analysis tools and triclinic boxes (Justin Lemkul) > 6. Re: TFE-water simulation (Archana Sonawani-Jagtap) > 7. Re: Gentle heating with implicit solvent (Gianluca Interlandi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 4 Nov 2013 17:05:36 +0100 > From: Mark Abraham <mark.j.abra...@gmail.com> > Subject: Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster > cluster with centos 6.0 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAMNuMAQcWLcKA=GPG1Ewr8s4A=PoTGOSWaqa= > s_uzbyw8uf...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta <bharat.85.m...@gmail.com > >wrote: > > > Hi, > > > > I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works > > fine till .configure command, but I am getting error at the make command > :- > > > > Error: > > ==================== > > [root@cluster gromacs-4.5.7]# make > > > > These is no need to run make as root - doing so guarantees you have almost > no knowledge of the final state of your entire machine. > > > > /bin/sh ./config.status --recheck > > running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi > > LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create > > --no-recursion > > checking build system type... x86_64-unknown-linux-gnu > > checking host system type... x86_64-unknown-linux-gnu > > ./configure: line 2050: syntax error near unexpected token `tar-ustar' > > ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' > > make: *** [config.status] Error 2 > > > > Looks like the system has an archaic autotools setup. Probably you can > comment out the line with tar-ustar from the original configure script, or > remove tar-ustar. Or use the CMake build. > > > > > > > > I have another query regarding the gromacs that comes with the Rocks > > cluster distribution. The mdrun of that gromacs has been complied without > > mpi option. How can I recomplie with mpi option. As I need the .configure > > file which is not there in the installed gromacs folder of the rocks > > cluster ... > > > > The 4.5-era GROMACS installation instructions are up on the website. > Whatever's distributed with Rocks is more-or-less irrelevant. > > Mark > > > > > > > > Thanks in advance for help > > > > > > > > > > Regards > > ------------ > > Bharat > > -- > > 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 > > > > > ------------------------------ > > Message: 2 > Date: Mon, 4 Nov 2013 11:29:43 -0700 > From: Stephanie Teich-McGoldrick <stephani...@gmail.com> > Subject: [gmx-users] Analysis tools and triclinic boxes > To: gmx-users@gromacs.org > Message-ID: > <CAF3rbpYDH-79tjESREDNzxJHSdGTV9q6=m+v= > c3asvwseop...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear all, > > I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail > list, it is my understanding that the default box shape in gromacs in a > triclinic box. Can I assume that all the analysis tools also work for a > triclinic box. > > Cheers, > Stephanie > > > ------------------------------ > > Message: 3 > Date: Mon, 4 Nov 2013 10:29:06 -0800 (PST) > From: Steve Seibold <steve...@ymail.com> > Subject: [gmx-users] Group protein not found in indexfile > To: gmx-users@gromacs.org > Message-ID: > <1383589746.69990.yahoomailba...@web140503.mail.bf1.yahoo.com> > Content-Type: text/plain; charset=utf-8 > > Hello > I am just trying to do a simple MD on a dimmer system (in which the > dimmers are NOT identical). I can use pdb2gmx to create a topology file and > four .itp files:::: pores.chainA.itp, pores.chainX.itp; > system.Protein.chainA.itp and system.Protein.chainX.itp. > > When I use grompp however, I get a fatal error “Group protein not found > in index file. Maybe you have non-default groups in your .mdp file, while > not using ‘-n’ option in grompp” > > I’ve looked up this error on-line but I don’t see people getting this > error when using multiple chains. I only have protein present and nothing > else. I am obviously doing something incorrect. > > I would greatly appreciate any comments that would help me.. > > Thanks. > > > > > ------------------------------ > > Message: 4 > Date: Mon, 04 Nov 2013 13:32:22 -0500 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Group protein not found in indexfile > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <5277e836.6050...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 11/4/13 1:29 PM, Steve Seibold wrote: > > Hello > > I am just trying to do a simple MD on a dimmer system (in which the > dimmers are NOT identical). I can use pdb2gmx to create a topology file and > four .itp files:::: pores.chainA.itp, pores.chainX.itp; > system.Protein.chainA.itp and system.Protein.chainX.itp. > > > > When I use grompp however, I get a fatal error “Group protein not found > in index file. Maybe you have non-default groups in your .mdp file, while > not using ‘-n’ option in grompp” > > > > I’ve looked up this error on-line but I don’t see people getting this > error when using multiple chains. I only have protein present and nothing > else. I am obviously doing something incorrect. > > > > I would greatly appreciate any comments that would help me.. > > > > Please provide: > > 1. Your exact grompp command > 2. Your full .mdp file > 3. The gmxcheck output of the .ndx file > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > Message: 5 > Date: Mon, 04 Nov 2013 13:32:52 -0500 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Analysis tools and triclinic boxes > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <5277e854.9000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote: > > Dear all, > > > > I am using gromacs 4.6.3 with a triclinic box. Based on the manual and > mail > > list, it is my understanding that the default box shape in gromacs in a > > triclinic box. Can I assume that all the analysis tools also work for a > > triclinic box. > > > > All analysis tools should work correctly for all box types. Is there a > specific > issue you are having, or just speculation? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > Message: 6 > Date: Tue, 5 Nov 2013 00:25:38 +0530 > From: Archana Sonawani-Jagtap <ask.arch...@gmail.com> > Subject: Re: [gmx-users] TFE-water simulation > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > cafv47mi+m372dpqycqzpdsgyg+y7rdmpbfgq5c4d9bmplly...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Thanks Joao Henriques for helping me with the steps. > On Nov 4, 2013 3:18 PM, "João Henriques" <joao.henriques.32...@gmail.com> > wrote: > > > Hello Archana, > > > > I'm also toying with a TFE-water system, therefore I am also a newbie. > This > > is what I am doing, I hope it helps: > > > > 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I > > don't use PRODGR, see why in DOI: 10.1021/ci100335w). > > 2) Do the math and check how many molecules of TFE you're going to need > for > > a given v/v TFE-water ratio and a given simulation box volume. > > 3) Build box with the correct size. > > 4) Randomly insert correct number of TFE molecules. > > 5) Solvate. > > 6) Insert protein. > > > > Hopefully, the amount of TFE and water molecules that will be deleted in > > inserting the protein in the final step will be proportional, given that > > the TFE molecules are well distributed. > > > > I've tried many different ways of doing this and it's always impossible > to > > maintain a perfect TFE-water ratio, no matter the order and manner of > > insertion of each system component. I've also never been able to insert > the > > correct number of waters after the TFE. My calculations predict a higher > > number, but the solvation algorithm can't find enough space for them. > > > > In sum, either you place each molecule by hand and you spend a life time > > building the system, or you just make a few compromises and deal with > it. I > > ended up going with the former as I have a limited amount of time on my > > hands and I am aware of the approximations I am doing. > > > > Best regards, > > > > João Henriques > > ------------------------------------------------ > > PhD student > > Division of Theoretical Chemistry > > Lund University > > Lund, Sweden > > ------------------------------------------------ > > joao.henriq...@teokem.lu.se > > http://www.teokem.lu.se/~joaoh/ > > > > > > On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: > > > > > >> Dear Justin, > > >> > > >> I have not constructed the system but I have downloaded it from ATB > > >> website. To maintain the number of TFE and water molecules(1:1 v/v) in > > the > > >> system (I don't want to add extra water molecules) I tried many > options > > in > > >> genbox but still it adds 678 water molecules. Can you provide me some > > >> hint? > > >> > > >> > > > Not without seeing your actual command(s). > > > > > > > > > Is their need to remove periodicity of this pre-equilibrated system as > > in > > >> case of lipids? > > >> > > >> > > > No idea. Are the molecules broken in the initial configuration? > > > > > > -Justin > > > > > > -- > > > ================================================== > > > > > > > > > Justin A. Lemkul, Ph.D. > > > Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 601 > > > University of Maryland, Baltimore > > > 20 Penn St. > > > Baltimore, MD 21201 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > > > ================================================== > > > > > > -- > > > 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 > > > > > -- > > 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 > > > > > ------------------------------ > > Message: 7 > Date: Mon, 4 Nov 2013 11:25:32 -0800 (PST) > From: Gianluca Interlandi <gianl...@u.washington.edu> > Subject: Re: [gmx-users] Gentle heating with implicit solvent > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > alpine.lnx.2.00.1311041112100.17...@artemide.bioeng.washington.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Dear Mark, > > Sorry for replying to an older thread. We are trying to perform implicit > solvent simulations of protein G with CHARMM27 in gromacs. We are trying > to trouble shoot why the protein unfolds after already 2 ns of dynamics. > We use simulated annealing for the heating with 1 fs time step. The > thermostat is v_rescale and OBC is the GBSA algorithm. Do you have any > suggestions what we could improve? You mention using a sub-fs time step > for the equilibration. Do you still use LINCS? Do you use simulated > annealing to heat up the system or do you just apply position restraints > to the heavy atoms? > > Thanks, > > Gianluca > > On Wed, 28 Aug 2013, Mark Abraham wrote: > > > It can be. Lack of explicit degrees of freedom of solvent can make > > achieving equipartition tricky. With CHARMM27 and virtual sites in > implicit > > solvent, I have sometimes found it necessary to use a sub-femtosecond > time > > step at the start of equilibration, even where there were no atomic > > clashes. Maybe the system was just unlucky with generating velocities, > > though :-) > > > > Mark > > On Aug 28, 2013 7:16 AM, "Gianluca Interlandi" < > gianl...@u.washington.edu> > > wrote: > > > >> How important is it to do gentle heating (using simulated annealing) > with > >> GBSA? Often with explicit water it is enough to perform some > equilibration > >> with positional restraints. Would it be enough to do the same with > implicit > >> solvent? > >> > >> Thanks, > >> > >> Gianluca > >> > >> ------------------------------**----------------------- > >> Gianluca Interlandi, PhD gianl...@u.washington.edu > >> +1 (206) 685 4435 > >> http://artemide.bioeng.**washington.edu/< > http://artemide.bioeng.washington.edu/> > >> > >> Research Scientist at the Department of Bioengineering > >> at the University of Washington, Seattle WA U.S.A. > >> http://healthynaturalbaby.org > >> ------------------------------**----------------------- > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > >> * Please search the archive at http://www.gromacs.org/** > >> Support/Mailing_Lists/Search< > 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< > http://www.gromacs.org/Support/Mailing_Lists> > >> > > -- > > 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 > > > > ----------------------------------------------------- > Gianluca Interlandi, PhD gianl...@u.washington.edu > +1 (206) 685 4435 > http://artemide.bioeng.washington.edu/ > > Research Scientist at the Department of Bioengineering > at the University of Washington, Seattle WA U.S.A. > ----------------------------------------------------- > > > ------------------------------ > > -- > 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 115, Issue 16 > ****************************************** > -- 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
