[gmx-users] Re: ATP

Graham Smith smithgr at cancer.org.uk
Fri Feb 14 23:27:01 CET 2003


Hi - 

There have been a couple of messages about ADP and ATP  in the last 
couple of days. 

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... 

-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:

> Send gmx-users mailing list submissions to
> 	gmx-users at 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
> 	gmx-users-request at gromacs.org
> 
> You can reach the person managing the list at
> 	gmx-users-admin at 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: 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
> 




More information about the gromacs.org_gmx-users mailing list