[gmx-users] No such moleculetype Na
Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. any help will highly appreciated. -- gmx-users mailing listgmx-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
Re: [gmx-users] No such moleculetype Na
On 11/12/2011 8:17 PM, Setare Jiji wrote: Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. Then you were either not looking at the right file, or not looking at the right name. As genion -h says, you need to use the molecule name, not the atom name or residue name. Mark -- gmx-users mailing listgmx-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] coordinate number aroud the first shell
Dear Prof. I want to obtain the coordinate number from the first shell around my cluster, I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr) until the first minimum of the RDF, but I have some questions: Please help me 1- How do I obtain the number density for special rdf? by g_density? how? 2- After this, should I compute N (coordinate number) manually? Best Regards Sara -- gmx-users mailing listgmx-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] trjconv -pbc mol/nojump
Hi, I have run simulation of a large solute in a box of water. Trying to look at the simulation output I used trjconv with and without the -pbc nojump option. For example: (1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_pbcmol.pdb -pbc mol -ur compact (2) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_nojump.pdb -pbc nojump With pbc=mol the solute is broken to few pieces, while the water molecules are placed in a box with few holes. With pbc=nojump the solute seems reasonably well but the water molecules are scattered in a large radius around the solute, and some of them are not broken (OH or H). I tried many options of trjconv and read the 'suggested trjconv workflow' but I still can't obtain a reasonable complete system after the simulation. How can I solve this problem? Thanks, Efrat -- gmx-users mailing listgmx-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
Re: [gmx-users] trjconv -pbc mol/nojump
On 11/12/2011 11:23 PM, Efrat Exlrod wrote: Hi, I have run simulation of a large solute in a box of water. Trying to look at the simulation output I used trjconv with and without the -pbc nojump option. For example: (1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_pbcmol.pdb -pbc mol -ur compact (2) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_nojump.pdb -pbc nojump With pbc=mol the solute is broken to few pieces, while the water molecules are placed in a box with few holes. With pbc=nojump the solute seems reasonably well but the water molecules are scattered in a large radius around the solute, and some of them are not broken (OH or H). I tried many options of trjconv and read the 'suggested trjconv workflow' but I still can't obtain a reasonable complete system after the simulation. How can I solve this problem? This is a straightforward situation where the suggested workflow works: remove jumps (so all molecules are whole), then center on the solute, and then put everything in some box (so -pbc mol, which leaves the centered solute where it is). Mark -- gmx-users mailing listgmx-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
回复： [gmx-users] No such moleculetype Na
The name of ion is different when using different force field You can check which field force you use and find out how Na and Cl ion is written in this force field. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年12月11日，周日, Setare Jiji jj.64fh...@yahoo.com 写道： 发件人: Setare Jiji jj.64fh...@yahoo.com 主题: [gmx-users] No such moleculetype Na 收件人: gmx-users@gromacs.org 日期: 2011年12月11日,周日,下午5:17 Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. any help will highly appreciated. -下面为附件内容- -- 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 listgmx-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] trjconv -pbc mol/nojump
Hi, You should use trjconv in 2 steps: (1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_pbc_nojump.xtc -pbc nojump in this step, select system for output (2) trjconv_d -s md_100ns.tpr -f md_100ns_pbc_nojump.xtc -o md_100ns_pbc_mol_center.xtc -pbc mol -center in this step, select solute for centering and system for output. I hope it help you -- gmx-users mailing listgmx-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
Re: 回复： [gmx-users] No such moleculetype Na
On 11/12/2011 11:43 PM, yp sun wrote: The name of ion is different when using different force field You can check which field force you use and find out how Na and Cl ion is written in this force field. The molecule name is constant over all force fields in the 4.5 series of GROMACS, and the molecule name is all that genion cares about. Atom and residue names might vary. Mark Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- *11年12月11日，周日, Setare Jiji /jj.64fh...@yahoo.com/* 写道： 发件人: Setare Jiji jj.64fh...@yahoo.com 主题: [gmx-users] No such moleculetype Na 收件人: gmx-users@gromacs.org 日期: 2011年12月11日,周日,下午5:17 Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. any help will highly appreciated. -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc156.mail.yahoo.com/mc/compose?to=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 http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] No such moleculetype Na
Did you try NA or CL. All caps worked for me last time I used this. Egy On Dec 11, 2011, at 4:17 AM, Setare Jiji wrote: Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. any help will highly appreciated. -- gmx-users mailing listgmx-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 listgmx-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
RE: [gmx-users] coordinate number aroud the first shell
1 - number of atoms divided by size of the box. 2 - manually or via a script. I have a script set up within Sigma Plot that I use for mine, but can be done in any other spreadsheet and programming language too. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Sunday, 11 December 2011 11:15 PM To: gmx-users@gromacs.org Subject: [gmx-users] coordinate number aroud the first shell Dear Prof. I want to obtain the coordinate number from the first shell around my cluster, I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr) until the first minimum of the RDF, but I have some questions: Please help me 1- How do I obtain the number density for special rdf? by g_density? how? 2- After this, should I compute N (coordinate number) manually? Best Regards Sara -- gmx-users mailing listgmx-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
Re: [gmx-users] coordinate number aroud the first shell
Dear Prof. Thank you very much for your reply. Excuse me, I saw a figure in one article that showed the number density distribution for the surfactant molecules' angles for the production run. how? Is this as same as number density for coordinate number?how? And some of articles with gromacs have a figure of radial density and radial number density and density as r(distance), I think those have been obtained with g_rdf, but how as a figure? Please help me. Best Regards Sara From: Dallas Warren dallas.war...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, December 12, 2011 12:38 AM Subject: RE: [gmx-users] coordinate number aroud the first shell 1 – number of atoms divided by size of the box. 2 – manually or via a script. I have a script set up within Sigma Plot that I use for mine, but can be done in any other spreadsheet and programming language too. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Sunday, 11 December 2011 11:15 PM To: gmx-users@gromacs.org Subject: [gmx-users] coordinate number aroud the first shell Dear Prof. I want to obtain the coordinate number from the first shell around my cluster, I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr) until the first minimum of the RDF, but I have some questions: Please help me 1- How do I obtain the number density for special rdf? by g_density? how? 2- After this, should I compute N (coordinate number) manually? Best Regards Sara -- 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 listgmx-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] Information about g_sas
Dear all Which is the difference between hydropilic and hydrophobic sas? How can give an interpretation to g_sas xvg graph? What can I find out in it and how can use g_sas to analyze a trajectory? Thanks-- gmx-users mailing listgmx-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] g_hbond
Dear gromacs users, I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate in water. Following is the output I obtained for the polycarboxylate H-bondign with water ACF 36008/36008 Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.000661899 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.300 3.334 7.513 0.000661899 Backward1.608 0.622 3.350 One-way 0.089 11.284 10.536 Integral0.039 25.374 12.544 Relaxation 0.062 16.080 11.413 I have read David paper (2006) on thermodynamics of H-bonding. In the paper two delta G values are mentioned. one is the Gibbs energy of activation (dG#) and another is the free energy of H-bonding. In the output given from the -ac analysis, which dG values do these correspond to? I assumed dG given for the forward rate correspond to the energy of activation. Is it correct? What is the value for free energy of H-bonding. Another question I have is, for a polycarboxylic acid system in water (COOH groups as side chains) for a 10ns run, I got the following as the output where the life time of the H-bond (between the polyacid and water) is negative. Is this correct? ACF 22057/22057 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0146697 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward-0.271 -3.687-666.000 0.0146697 Backward -2.291 -0.437-666.000 One-way 0.101 9.882 10.207 Integral0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- gmx-users mailing listgmx-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] Gromacs Installation error
Hi gromacs users,
Iam trying to install gromacs on IBM cluster. I have successfully installed
installed fftw-3.3 version with commands=
./configure --enable-threads --enable-float
make
make install
the set the enviroment=
setenv CPPFLAGS -I/home/fftw/include
setenv LDFLAGS -L/home/fftw/lib
Then the gromacs installation=
./configure --prefix=/home/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC=mpCC CC=xlC_r -q64 CFLAGS=-O3
-qarch=ppc64 -qtune=auto CXX=xlC_r -q64 CXXFLAGS=-O3 -qarch=ppc64
-qtune=auto F77=mpixlf_r FFLAGS=-O3 -qarch=ppc64 -qtune=auto
the configure did well but while doing make mdrun i started getting
error such as=
source='vmdio.c' object='vmdio.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H
-I. -I../../src -I../../include
-DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3
-qarch=ppc64 -qtune=auto -c -o vmdio.lo vmdio.c
mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3
-qarch=ppc64 -qtune=auto -c vmdio.c -o vmdio.o
1506-503 (W) Option -qlongdouble / -qldbl128 is not supported for
LINUX for Power.
/usr/include/glob.h, line 166.34: 1506-276 (S) Syntax error:
possible missing identifier?
/usr/include/glob.h, line 166.12: 1506-033 (S) Function
__REDIRECT_NTH is not valid. Function cannot return a function.
/usr/include/glob.h, line 166.12: 1506-282 (S) The type of the
parameters must be specified in a prototype.
/usr/include/glob.h, line 169.35: 1506-334 (S) Identifier glob_t has
already been defined on line 113 of /usr/include/glob.h.
/usr/include/glob.h, line 169.42: 1506-277 (S) Syntax error:
possible missing ';' or ','?
/usr/include/glob.h, line 171.39: 1506-276 (S) Syntax error:
possible missing identifier?
/usr/include/glob.h, line 171.13: 1506-282 (S) The type of the
parameters must be specified in a prototype.
/usr/include/glob.h, line 171.13: 1506-343 (S) Redeclaration of
__REDIRECT_NTH differs from previous declaration on line 166 of
/usr/include/glob.h.
/usr/include/glob.h, line 171.13: 1506-050 (I) Return type void in
redeclaration is not compatible with the previous return type
int(const char*,int).
/usr/include/glob.h, line 171.58: 1506-160 (S) Object globfree64
cannot be declared as type void.
/usr/include/glob.h, line 175.12: 1506-343 (S) Redeclaration of
glob64 differs from previous declaration on line 169 of
/usr/include/glob.h.
/usr/include/glob.h, line 175.12: 1506-382 (I) The type int(const
char* restrict,int,int(*)(const char*,int),struct {...}* restrict) of
identifier glob64 differs from previous type int.
make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib make ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/mdlib'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed
by `libmd_mpi.la'. Stop.
make[1]: Leaving directory `/home/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
/bin/sh ../../libtool --tag=CC --mode=link mpCC -O3 -qarch=ppc64
-qtune=auto -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath
/home/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo
gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo
pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo
ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo
topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo
../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
unhandled argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory `/home/gromacs-4.5.5/src/kernel'
please help!
Aiswarya
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Re: [gmx-users] g_hbond
On 2011-12-12 07:41, sulatha M. S wrote: Dear gromacs users, I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate in water. Following is the output I obtained for the polycarboxylate H-bondign with water ACF 36008/36008 Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.000661899 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.300 3.334 7.513 0.000661899 Backward1.608 0.622 3.350 One-way 0.089 11.284 10.536 Integral0.039 25.374 12.544 Relaxation 0.062 16.080 11.413 I have read David paper (2006) on thermodynamics of H-bonding. In the paper two delta G values are mentioned. one is the Gibbs energy of activation (dG#) and another is the free energy of H-bonding. In the output given from the -ac analysis, which dG values do these correspond to? I assumed dG given for the forward rate correspond to the energy of activation. Is it correct? What is the value for free energy of H-bonding. Yes it is DGact. The DGeq follows from the fraction of COOH that are not forming hydrogen bonds, option -nhbdist. Another question I have is, for a polycarboxylic acid system in water (COOH groups as side chains) for a 10ns run, I got the following as the output where the life time of the H-bond (between the polyacid and water) is negative. Is this correct? This means that the ACF has not equilibrated and you need much longer sims. You probably got a warning about it. ACF 22057/22057 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0146697 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward-0.271 -3.687-666.000 0.0146697 Backward -2.291 -0.437-666.000 One-way 0.101 9.882 10.207 Integral0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
