[gmx-users] Re: ATP
David
spoel at xray.bmc.uu.se
Mon Feb 17 07:51:12 CET 2003
> There are some features of the ATP in ffgmx that look a little
> half-finished - eg hydrogens are not added to the aromatic system, as
> seems to be usual with the gromos forcefields, and none of the
> hydrogens (not even those on the hydroxyl oxygens on the ribose) are
> in the hdb file. I have done a fair bit of work on putting ADP and ATP
> into the ffG43 force field, and have something that works, with
> automatic polar H addition to hydroxyls and aromatics. Simulations in
> water or as a protein ligand seem OK (in water, with more than one
> molecule, you sometimes get spontaneous base-stacking) but I could
> never find force constants that stopped the di- and tri-phosphates
> from bending in an unreasonable looking way (0-P-O angles a low as 60
> degrees etc), especially when MG^2+ was present (as I believe it
> always is physiologically). I don't know whether this is due to the
> funny way Gromacs 96 does its angle potentials. Anyway, please contact
> me if you want these files, I'm happy to give them to anybody who
> wants them; it might save some work, but you'll have to do a bit of
> further development yourself...
Could this angle bending be due to the 1-4 Coulomb interaction between H
and O in a phosphate group? We generally turn such interactios off.
> -Graham
>
> ########################################################################
>
> Dr. Graham R. Smith,
> Biomolecular Modelling Laboratory,
> Cancer Research UK,
> 44 Lincoln's Inn Fields,
> London WC2A 3PX,
> U.K.
> Tel: +44-(0)20 7269 3348
> email: graham.smith at cancer.org.uk
> URL: http://www.bmm.icnet.uk/~smithgr
>
>
> On Fri, 14 Feb 2003 gmx-users-request at gromacs.org wrote:
>
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> > than "Re: Contents of gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: crash in double precision GROMACS (Claudio Arlandini)
> > 2. Re: about *.gro file (Valentin Gogonea)
> > 3. Re: sgi -r12000 flag (Arvid Soederhaell)
> > 4. NMA in vaccum or water? (Berk Hess)
> > 5. Re: sgi -r12000 flag (David van der Spoel)
> > 6. Re: crash in double precision GROMACS (Claudio Arlandini)
> > 7. Re: sgi -r12000 flag (Arvid Soederhaell)
> > 8. Two Sodium ions in ATP file (Mike Jargas)
> > 9. Re: about *.gro file (tivi)
> > 10. Re: Two Sodium ions in ATP file (David)
> > 11. compile error - MAC OSX (Steven Hentel)
> > 12. heat up the system (Juntao Guo)
> > 13. Re: compile error - MAC OSX (Erik Lindahl)
> >
> > --__--__--
> >
> > Message: 1
> > Date: Fri, 14 Feb 2003 12:34:38 +0100
> > From: Claudio Arlandini <arlandini at cilea.it>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Re: crash in double precision GROMACS
> > Reply-To: gmx-users at gromacs.org
> >
> > Here is the debugger (gdb) output.
> > I compiled with CFLAGS "-g" ,HP compilers and MPI libraries
> > with configure --enable-mpi --disable-float --without-x
> > BTW: in my makelog file it results gmxfio.c is compiled and without errors.
> >
> > ------------------------
> >
> > Division over nodes in atoms:
> > 7600 7600 7600 7600 7600 7600 7625 7626 7626 7626 7626 7626
> > 7626 7626 7626 7623
> > writing run input file...
> >
> > Back Off! I just backed up 1md.tpr to ./#1md.tpr.2#
> >
> > Program received signal SIGBUS, Bus error.
> > 0x7fe18 in do_xdr (item=0x40044474 "", nitem=1, eio=0, desc=0x40016c98
> > "ir->epsilon_surface", srcfile=0x40016cb0 "tpxio.c",
> > line=186) at gmxfio.c:520
> > 520 gmxfio.c: No such file or directory.
> >
> >
> > (gdb) bt
> > #0 0x7fe18 in do_xdr (item=0x40044474 "", nitem=1, eio=0, desc=0x40016c98
> > "ir->epsilon_surface",
> > srcfile=0x40016cb0 "tpxio.c", line=186) at gmxfio.c:520
> > #1 0x59544 in do_inputrec (ir=0x40044408, bRead=0) at tpxio.c:186
> > #2 0x61ae4 in do_tpx (fp=0, bRead=0, step=0x70bd2cc8, t=0x70bd2cc0,
> > lambda=0x70bd2cb8, ir=0x40044408, box=0x70bd1aa0,
> > natoms=0x70bd2cac, x=0x434dfeb0, v=0x437a9eb8, f=0x0, top=0x40052230)
> > at tpxio.c:820
> > #3 0x62080 in write_tpx (fn=0x40049930 "1md.tpr", step=0, t=0, lambda=0,
> > ir=0x40044408, box=0x70bd1aa0, natoms=121856,
> > x=0x434dfeb0, v=0x437a9eb8, f=0x0, top=0x40052230) at tpxio.c:882
> > #4 0x30158 in main (argc=1, argv=0x70bd0aa4) at grompp.c:1008
> >
> >
> > Thanks, Claudio
> >
> >
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> > Dr. Claudio Arlandini, PhD \ C onsorzio
> > System Administration \ I nteruniversitario
> > \ L ombardo per la
> > e-mail arlandini at cilea.it \ E laborazione
> > ph. +39 02 26995.246 (fax +39 02 2135520) \ A utomatica
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\/~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> >
> >
> > --__--__--
> >
> > Message: 2
> > Date: Fri, 14 Feb 2003 06:55:55 -0500
> > From: Valentin Gogonea <v.gogonea at csuohio.edu>
> > Subject: Re: [gmx-users] about *.gro file
> > To: gmx-users at gromacs.org
> > Reply-To: gmx-users at gromacs.org
> >
> >
> > --Boundary_(ID_5Y4K6xqOPIcksEyJtjrgCg)
> > Content-type: text/plain; format=flowed; charset=US-ASCII
> > Content-transfer-encoding: 7BIT
> >
> > Did anybody had a problem with this file?
> >
> > Valentin Gogonea
> > CSU
> >
> > On Friday, February 14, 2003, at 02:06 AM, Jinzhi Tan wrote:
> >
> > > VIRUS INFECTION ALERT
> > >
> > > The Cleveland State University virus scanning system has discovered a
> > > virus in the file originally attached to this email. The file was not
> > > able to be cleaned and has been removed. You may wish to contact the
> > > sender of this email to advise them of the problem.
> > >
> > > File name: noname.txt
> > > Virus name: No status string available
> > >
> >
> > --Boundary_(ID_5Y4K6xqOPIcksEyJtjrgCg)
> > Content-type: text/enriched; charset=US-ASCII
> > Content-transfer-encoding: 7BIT
> >
> > Did anybody had a problem with this file?
> >
> >
> > Valentin Gogonea
> >
> > CSU
> >
> >
> > On Friday, February 14, 2003, at 02:06 AM, Jinzhi Tan wrote:
> >
> >
> > <excerpt><bold><color><param>FFFF,0000,0000</param><bigger><bigger><bigger><bigger><bigger><bigger>VIRUS
> > INFECTION ALERT</bigger></bigger></bigger></bigger></bigger></bigger></color></bold>
> >
> >
> > The Cleveland State University virus scanning system has discovered a
> > virus in the file originally attached to this email. The file was not
> > able to be cleaned and has been removed. You may wish to contact the
> > sender of this email to advise them of the problem.
> >
> >
> > File name: noname.txt
> >
> > Virus name: No status string available
> >
> >
> > </excerpt>
> >
> > --Boundary_(ID_5Y4K6xqOPIcksEyJtjrgCg)--
> >
> > --__--__--
> >
> > Message: 3
> > Date: Fri, 14 Feb 2003 13:09:35 +0100 (MET)
> > From: Arvid Soederhaell <arvid at fmp-berlin.de>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] sgi -r12000 flag
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi again List
> > The compilation problem was unfortunately not solved by the
> > suggested flags. The compilation get stuck in the same position, that is
> > in the protonate.c subroutine. It is strange that the error messages
> > starts at the first commentary ending command "*/" since exactly the same
> > thing is written in the head of all other programs.
> >
> > I didn't mentioned it in the e-mail below but the logn row of error
> > messages ends by:
> >
> > -----------------------------------------------------------------------
> > "protonate.c", line 113: error(1007): unrecognized token
> > /* check input */
> > ^
> >
> >
> > Error limit reached. 100 errors detected in the compilation of "protonate.c".
> > Compilation terminated.
> > *** Error code 2 (bu21)
> > *** Error code 1 (bu21)
> > *** Error code 1 (bu21)
> > *** Error code 1 (bu21)
> > ------------------------------------------------------------------------
> >
> > I dont know if that adds any new information, but for completeneness it
> > should be mentioned.
> >
> > Any suggestions how to solve this problem are certainly welcome!
> >
> > Thanks
> > Arvid
> >
> >
> >
> >
> > > Arvid Soederhaell wrote:
> > >
> > > Hi Arvid,
> > >
> > > Try setting CFLAGS="-mips4 -O3 -r10000 -woff 1174" (and FFLAGS) before
> > > running the configure script, and then recompile.
> > >
> > > Cheers,
> > >
> > > Erik
> > >
> > > >Hi gromacs users
> > > >
> > > >I'm trying to install gromacs 3.1.4 on an SGI origin having R12000 CPU's.
> > > >The configure script detects the cpu type but I get the following message:
> > > >
> > > >-----------------------------------------------------------------------
> > > >MIPSpro Compilers: Version 7.2.1 checking whether cc accepts -r12000
> > > >-mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead
> > > >-INLINE:=ON -LNO:opt=1 -LNO:ou_further=3
> > > >-OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS...
> > > >no
> > > >******************************************************************* *
> > > >Sorry, these optimization settings don't seem to work for * * your C
> > > >compiler. Use make CFLAGS=..., or edit the top Makefile. *
> > > >*******************************************************************
> > > >checking whether f77 accepts -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3
> > > >-OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3
> > > >-OPT:Olimit=0:roundoff=3:alias=typed -OPT:cray_ivdep=TRUE... f77 ERROR
> > > >parsing -r12000: unknown flag yes
> > > >-------------------------------------------------------------------------
> > > >
> > > >The run ends with the message:
> > > >
> > > >-------------------------------------------------------------------------
> > > >configure: error: No math library found
> > > >-------------------------------------------------------------------------
> > > >
> > > >Since it says "ERROR parsing -r12000: unknown flag" i have edited the
> > > >configure script and replaced the -r12000 by -r10000. This works
> > > >relatively fine (quite afew warnings though) until the compilation reaches
> > > >the "protonate.c" subroutine where the error messages are
> > > >
> > > >------------------------------------------------------------------------
> > > >protonate.c", line 31: error(1007): unrecognized token
> > > > */
> > > > ^
> > > >
> > > >
> > > >
> > > >"protonate.c", line 31: error(1166): expected a declaration
> > > > */
> > > > ^
> > > >
> > > >"protonate.c", line 32: error(1007): unrecognized token
> > > > static char *SRCID_protonate_c = "$Id: protonate.c,v 1.5.2.1 2002/04/01
> > > >20:20:42 lindahl Exp $";
> > > >
> > > >^
> > > >
> > > >"protonate.c", line 32: error(1166): expected a declaration
> > > > static char *SRCID_protonate_c = "$Id: protonate.c,v 1.5.2.1 2002/04/01
> > > >20:20:42 lindahl Exp $";
> > > >
> > > >^
> > > >
> > > >"protonate.c", line 33: warning(1014): extra text after expected end of
> > > > preprocessing directive
> > > > #include <math.h>
> > > >--------------------------------------------------------------------------
> > > >
> > > >and so on...
> > > >
> > > >I have seen that there have been problems with the -n32 flag for SGI's,
> > > >but this does not seem to be related to that, or? Is it wrong or does it
> > > >make the code substantially slower when using the -r10000 flag? Any ideas
> > > >how to solve the problem?
> > > >
> > > >I have seen that there is a hack for sgi's in the configure script
> > > >suggesting --disable-waterwater-loops and --disable-waterloop-unrolling. I
> > > >dont really understand what that means, but it doesn't make a difference
> > > >if i include them upun installing.
> > > >
> > > >(I believe that the FFTW is properly installed in single precision.)
> > > >
> > > >Thanks in advance
> > > >
> > > > Arvid Soederhaell
> > > >
> > > >Arvid Soederhaell, PhD Phone:+49-30-94793-231
> > > >Forschungsinstitut fuerMolekulare Pharmakologie Mob:+49-160-9835 8282
> > > >Robert-Roessle-Strasse 10 Fax::+49-30-94793-169
> > > >131 25 Berlin (Mob:+46-70-723 33 63)
> > > >
> > > >_______________________________________________
> > > >gmx-users mailing list
> > > >gmx-users at gromacs.org
> > > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > > >Please don't post (un)subscribe requests to the list. Use the
> > > >www interface or send it to gmx-users-request at gromacs.org.
> > > >
> > > >
> > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --__--__--
> >
> > Message: 4
> > From: "Berk Hess" <gmx3 at hotmail.com>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] NMA in vaccum or water?
> > Date: Fri, 14 Feb 2003 14:09:05 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > >Ruben Martinez Buey wrote:
> > > > > Hi all,
> > > > > Sorry, I did not understand right,
> > > > > for energy minimization before NMA, do you recommendwater or vacuum?
> > > >
> > >
> > > > which Coulumb-type?
> > >
> > > >cut-off
> > >
> > > > which rcoulomb?
> > >
> > >5 nm (or something that is as least as large as the largest distance
> > >in your molecule)
> >
> > Or even better (and more efficient), use no cut-off:
> > pbc = none
> > nstlist = 0
> > rlist = 0
> > rcoulomb = 0
> > rvdw = 0
> >
> > Berk.
> >
> >
> >
> > _________________________________________________________________
> > STOP MORE SPAM with the new MSN 8 and get 2 months FREE*
> > http://join.msn.com/?page=features/junkmail
> >
> >
> > --__--__--
> >
> > Message: 5
> > Subject: Re: [gmx-users] sgi -r12000 flag
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > To: gmx-users at gromacs.org
> > Date: 14 Feb 2003 17:20:02 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > On Fri, 2003-02-14 at 13:09, Arvid Soederhaell wrote:
> > > Hi again List
> > > The compilation problem was unfortunately not solved by the
> > > suggested flags. The compilation get stuck in the same position, that is
> > > in the protonate.c subroutine. It is strange that the error messages
> > > starts at the first commentary ending command "*/" since exactly the same
> > > thing is written in the head of all other programs.
> > >
> > > I didn't mentioned it in the e-mail below but the logn row of error
> > > messages ends by:
> > >
> > > -----------------------------------------------------------------------
> > > "protonate.c", line 113: error(1007): unrecognized token
> > > /* check input */
> > > ^
> >
> > I just checked my protonate.c file, and it seems to be a MS-DOS file
> > (i.e. wrong end-of-line character). IIRC irix has a tool to fix this:
> > dos2unix filename
> >
> > try that on protonate.c
> >
> > --
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, Dept. of Cell & Mol. Biology
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > --__--__--
> >
> > Message: 6
> > Date: Fri, 14 Feb 2003 15:13:08 +0100
> > From: Claudio Arlandini <arlandini at cilea.it>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Re: crash in double precision GROMACS
> > Reply-To: gmx-users at gromacs.org
> >
> > I am sorry, I just realized I was working with version 3.1.3, and when I
> > tried 3.1.4 the program was running (at least with d.dppc).
> >
> > Only problem, I had to change variable name "fmax" in xutils.c into
> > something else (fmax_c), otherwise HP compiler complained and the
> > compilation halted.
> >
> > Thanks again,
> >
> > Claudio Arlandini
> >
> >
> >
> > --__--__--
> >
> > Message: 7
> > Date: Fri, 14 Feb 2003 16:10:15 +0100 (MET)
> > From: Arvid Soederhaell <arvid at fmp-berlin.de>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] sgi -r12000 flag
> > Reply-To: gmx-users at gromacs.org
> >
> > Thanks alot!!!
> > dos2unix was the key!!! The protonate.c file that came with the original
> > tar package (3.1.4) was in DOS format with the meta-charactrer at the end
> > of each line. I used the suggested dos2unix program for the conversion,
> > and now i can complile!!! Obviously my computer is quite sensitive to
> > that kind of problems.
> >
> > Thanks again!!!
> > Arvid
> >
> > Arvid Soederhaell, PhD Phone:+49-30-94793-231
> > Forschungsinstitut fuer Molekulare Pharmakologie Mob:+49-160-9835 8282
> > Robert-Roessle-Strasse 10 Fax::+49-30-94793-169
> > 131 25 Berlin (Mob:+46-70-723 33 63)
> >
> > On 14 Feb 2003, David van der Spoel wrote:
> >
> > > On Fri, 2003-02-14 at 13:09, Arvid Soederhaell wrote:
> > > > Hi again List
> > > > The compilation problem was unfortunately not solved by the
> > > > suggested flags. The compilation get stuck in the same position, that is
> > > > in the protonate.c subroutine. It is strange that the error messages
> > > > starts at the first commentary ending command "*/" since exactly the same
> > > > thing is written in the head of all other programs.
> > > >
> > > > I didn't mentioned it in the e-mail below but the logn row of error
> > > > messages ends by:
> > > >
> > > > -----------------------------------------------------------------------
> > > > "protonate.c", line 113: error(1007): unrecognized token
> > > > /* check input */
> > > > ^
> > >
> > > I just checked my protonate.c file, and it seems to be a MS-DOS file
> > > (i.e. wrong end-of-line character). IIRC irix has a tool to fix this:
> > > dos2unix filename
> > >
> > > try that on protonate.c
> > >
> > > --
> > > Groeten, David.
> > > ________________________________________________________________________
> > > Dr. David van der Spoel, Dept. of Cell & Mol. Biology
> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --__--__--
> >
> > Message: 8
> > From: "Mike Jargas" <dosstopher at hotmail.com>
> > To: gmx-users at gromacs.org
> > Date: Fri, 14 Feb 2003 12:08:15 -0500
> > Subject: [gmx-users] Two Sodium ions in ATP file
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi there,
> >
> > I am trying to use the new force field for a simulation. I want to put
> > Sodium ions in the simulation, but when I look in the ffoplsaa.atp file
> > there are two entries for Na+ ions. One is referenced by opls_405 and the
> > info on it says JACS 106, 903 (1984)
> > The other is referenced by opls_407 and the info says Aqvists cation.
> >
> > What is the difference between these two entries? Are they meant for
> > different types of simulations?
> >
> > Thanks a lot!
> >
> > Sincerely,
> > Chris
> >
> >
> >
> > _________________________________________________________________
> > The new MSN 8: smart spam protection and 2 months FREE*
> > http://join.msn.com/?page=features/junkmail
> >
> >
> > --__--__--
> >
> > Message: 9
> > Date: Fri, 14 Feb 2003 12:10:43 -0600
> > From: tivi <t.orban at csuohio.edu>
> > Subject: Re: [gmx-users] about *.gro file
> > To: gmx-users at gromacs.org
> > Reply-To: gmx-users at gromacs.org
> >
> >
> > --Boundary_(ID_cT+WskHxaOgvFqGL96XDUw)
> > Content-type: text/plain; format=flowed; charset=US-ASCII
> > Content-transfer-encoding: 7BIT
> >
> > Yes I got the same mail.
> >
> > On Friday, February 14, 2003, at 05:55 AM, Valentin Gogonea wrote:
> >
> > > Did anybody had a problem with this file?
> > >
> > > Valentin Gogonea
> > > CSU
> > >
> > > On Friday, February 14, 2003, at 02:06 AM, Jinzhi Tan wrote:
> > >
> > >> VIRUS INFECTION ALERT
> > >>
> > >> The Cleveland State University virus scanning system has discovered a
> > >> virus in the file originally attached to this email. The file was not
> > >> able to be cleaned and has been removed. You may wish to contact the
> > >> sender of this email to advise them of the problem.
> > >>
> > >> File name: noname.txt
> > >> Virus name: No status string available
> > >>
> > >
> >
> > --Boundary_(ID_cT+WskHxaOgvFqGL96XDUw)
> > Content-type: text/enriched; charset=US-ASCII
> > Content-transfer-encoding: 7BIT
> >
> > Yes I got the same mail.
> >
> >
> > On Friday, February 14, 2003, at 05:55 AM, Valentin Gogonea wrote:
> >
> >
> > <excerpt>Did anybody had a problem with this file?
> >
> >
> > Valentin Gogonea
> >
> > CSU
> >
> >
> > On Friday, February 14, 2003, at 02:06 AM, Jinzhi Tan wrote:
> >
> >
> > <excerpt><bold><color><param>FFFE,0000,0000</param><bigger><bigger><bigger><bigger><bigger><bigger>VIRUS
> > INFECTION ALERT</bigger></bigger></bigger></bigger></bigger></bigger></color></bold>
> >
> >
> > The Cleveland State University virus scanning system has discovered a
> > virus in the file originally attached to this email. The file was not
> > able to be cleaned and has been removed. You may wish to contact the
> > sender of this email to advise them of the problem.
> >
> >
> > File name: noname.txt
> >
> > Virus name: No status string available
> >
> >
> > </excerpt> </excerpt>
> >
> > --Boundary_(ID_cT+WskHxaOgvFqGL96XDUw)--
> >
> > --__--__--
> >
> > Message: 10
> > Subject: Re: [gmx-users] Two Sodium ions in ATP file
> > From: David <spoel at xray.bmc.uu.se>
> > To: gmx-users at gromacs.org
> > Date: 14 Feb 2003 20:06:51 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > On Fri, 2003-02-14 at 18:08, Mike Jargas wrote:
> > > Hi there,
> > >
> > > I am trying to use the new force field for a simulation. I want to put
> > > Sodium ions in the simulation, but when I look in the ffoplsaa.atp file
> > > there are two entries for Na+ ions. One is referenced by opls_405 and the
> > > info on it says JACS 106, 903 (1984)
> > > The other is referenced by opls_407 and the info says Aqvists cation.
> >
> > The Aqvist version is usually regarded as better, since the free
> > energies of solvation are rproduced better. Note that this depends on
> > use of cut-off etc. Please read the papers and judge for yourself!
> > >
> > > What is the difference between these two entries? Are they meant for
> > > different types of simulations?
> > >
> > > Thanks a lot!
> > >
> > > Sincerely,
> > > Chris
> > >
> > >
> > >
> > > _________________________________________________________________
> > > The new MSN 8: smart spam protection and 2 months FREE*
> > > http://join.msn.com/?page=features/junkmail
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, Dept. of Cell and Molecular Biology
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > --__--__--
> >
> > Message: 11
> > From: "Steven Hentel" <xenobach at hotmail.com>
> > To: gmx-users at gromacs.org
> > Date: Fri, 14 Feb 2003 12:09:48 -0800
> > Subject: [gmx-users] compile error - MAC OSX
> > Reply-To: gmx-users at gromacs.org
> >
> > Help! I'm no UNIX pro and compiling gromacs gives me:
> >
> > xutils.c:97: `fmax' redeclared as different kind of symbol
> > /usr/include/architecture/ppc/math.h:307: previous declaration of `fmax'
> > xutils.c:97: warning: `fmax' was declared `extern' and later `static'
> >
> > I've tried make with the -e flag and that doesn't help.
> >
> > Steven
> >
> >
> > _________________________________________________________________
> > Protect your PC - get McAfee.com VirusScan Online
> > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963
> >
> >
> > --__--__--
> >
> > Message: 12
> > Date: Fri, 14 Feb 2003 15:13:36 -0500
> > From: Juntao Guo <jguo at utk.edu>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] heat up the system
> > Reply-To: gmx-users at gromacs.org
> >
> > Dear all,
> >
> > Does anyone know how to heat the system up slowly from 0 to 300k?
> > Thanks.
> >
> > JT
> >
> >
> > --__--__--
> >
> > Message: 13
> > Date: Fri, 14 Feb 2003 12:34:58 -0800
> > From: Erik Lindahl <lindahl at stanford.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] compile error - MAC OSX
> > Reply-To: gmx-users at gromacs.org
> >
> > Steven Hentel wrote:
> >
> > > Help! I'm no UNIX pro and compiling gromacs gives me:
> > >
> > > xutils.c:97: `fmax' redeclared as different kind of symbol
> > > /usr/include/architecture/ppc/math.h:307: previous declaration of `fmax'
> > > xutils.c:97: warning: `fmax' was declared `extern' and later `static'
> > >
> > > I've tried make with the -e flag and that doesn't help.
> > >
> > > Steven
> > >
> > Hi Steven,
> >
> > This seems to be a bug in some system header files; fmax isn't a
> > reserved word, so we should be able to use it, but instead of banging
> > your head against it you can just change the 2-3 occurences of fmax in
> > xutils.c to fmax_gmx or something. This is already fixed in our CVS sources.
> >
> > Cheers,
> >
> > Erik
> >
> >
> >
> >
> >
> > --__--__--
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >
> >
> > End of gmx-users Digest
> >
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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