[gmx-users] Regarding Equilibration
Dear all, Could you please tell me what kind of error limit is accepted for running NVT and NPT equilibration in terms of Temperature, Pressure and Density. Thank you, With Regards, Ravi Kumar V IPC Dept., IISc, 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
Re: [gmx-users] Regarding Equilibration
Ravi Kumar Venkatraman wrote: Dear all, Could you please tell me what kind of error limit is accepted for running NVT and NPT equilibration in terms of Temperature, Pressure and Density. You should obtain the values you set as ref_t and ref_p if you've done equilibration properly and for a sufficient time. How far off are your results? It could be a combination of factors, but without knowing much more about your system, .mdp settings, and equilibration scheme, it's impossible to know whether or not you should get what you expect. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] (no subject)
Hello, I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- 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] strange vdw energy from rerun with GBSA model.
Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high ( 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol. It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected. I believe fitting or no-jump processing shall not change the energy at all. Any one has idea about this? -- 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 subject)
Nilesh Dhumal wrote: Hello, I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. You can use genconf -nbox to generate a grid of replicates, but this artificially ordered system will need an extremely long equilibration time. You can induce some randomness to the system with genconf -rot. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] strange vdw energy from rerun with GBSA model.
On 11/08/2011 12:29 AM, Da-Wei Li wrote: Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high ( 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol. Something is badly wrong - perhaps your treatment of periodicity in the rerun - but we don't have anywhere near enough information to know. It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected. I believe fitting or no-jump processing shall not change the energy at all. Any one has idea about this? As above. 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
Re: [gmx-users] strange vdw energy from rerun with GBSA model.
Dear Mark That is my thought too.To test this possibility, I created a mdp file without PBC and use trjconv -pbc nojump to make whole protein. From visualization in UCSF Chimera, the trajectory looks fine. But I still have some snapshot that have very high vdw energy. best dawei On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 12:29 AM, Da-Wei Li wrote: Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high ( 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol. Something is badly wrong - perhaps your treatment of periodicity in the rerun - but we don't have anywhere near enough information to know. It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected. I believe fitting or no-jump processing shall not change the energy at all. Any one has idea about this? As above. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Gromacs compilation
On 10/08/2011 4:58 AM, Anthony Cruz Balberdi wrote:
Dear User:
I compiled GROMACS with OPEN64 without problems, Now I want to compile
it using the ACML libraries to compare the performance
mdrun will be identical. Several tools would improve.
How I can compile gromacs using the ACML libraries?
I tried:
./configure CC=opencc CXX=openCC F77=openf90 CFLAGS=-O3 -OPT:Ofast
-march=barcelona -LGROMACS_SUITE/FFTW3.3_open64_sse2/lib
-LGROMACS_SUITE/ACML4.4.0/open64_64/lib
CPPFLAGS=-IGROMACS_SUITE/FFTW3.3_open64_sse2/include --with-fft=fftw3
--with-external-lapack --with-external-blas LIBS=-lacml
but it give me the following error:
configure:4430: opencc -O3 -OPT:Ofast -march=barcelona
-L/home/acruz/bin/GROMACS_SUITE/FFTW3.3_open64_sse2/lib
-L/home/acruz/bin/GROMACS_SUITE/ACM
L4.4.0/open64_64/lib
-I/home/acruz/bin/GROMACS_SUITE/FFTW3.3_open64_sse2/include
conftest.c -lacml 5
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `s_cmp'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `vcos'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `_F90_STOP'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `_FWF'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `vcosf'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `s_cat'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `__powii'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `__powdi'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `s_copy'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `_FRF'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `__powri'
/home/acruz/bin/GROMACS_SUITE/ACML4.4.0/open64_64/lib/libacml.so:
undefined reference to `_index90'
Looks like you're omitting some linking libraries ACML requires. Check
out its documentation and amend
your LIBS value.
Mark
collect2: ld returned 1 exit status
configure:4434: $? = 1
configure:4471: result:
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
| #define PACKAGE_URL
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug 9 14:22:58 EDT 2011
| #define BUILD_USER acruz@micro1
| #define BUILD_MACHINE Linux 2.6.34.7-0.5-desktop x86_64
| /* end confdefs.h. */
| #include stdio.h
| int
| main ()
| {
| FILE *f = fopen (conftest.out, w);
| return ferror (f) || fclose (f) != 0;
|
| ;
| return 0;
| }
configure:4477: error: in
`/home/acruz/bin/GROMACS_SUITE/development/gromacs-4.5.4':
configure:4481: error: C compiler cannot create executables
See `config.log' for more details.
How I could solve the problem?
Best regards,
Anthony Cruz
--
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[gmx-users] Re: RTILs
I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. GENCONF -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] strange vdw energy from rerun with GBSA model.
On 11/08/2011 1:18 AM, Da-Wei Li wrote: Dear Mark That is my thought too.To test this possibility, I created a mdp file without PBC and use trjconv -pbc nojump to make whole protein. From visualization in UCSF Chimera, the trajectory looks fine. But I still have some snapshot that have very high vdw energy. If all you've done is strip water, make molecules whole with trjconv -nojump from a reference configuration that had whole molecules, and use pbc = no in the .mdp file, then that sounds impossible. Mark best dawei On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 11/08/2011 12:29 AM, Da-Wei Li wrote: Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high ( 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol. Something is badly wrong - perhaps your treatment of periodicity in the rerun - but we don't have anywhere near enough information to know. It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected. I believe fitting or no-jump processing shall not change the energy at all. Any one has idea about this? As above. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] Constraints not working in pull code (sometimes, sometimes not)
Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 nsteps = 5125000 ; 10.250 ns nstcomm = 1 comm_mode = Linear ; Output parameters nstxout = 0 ; every 1 ns nstvout = 0 nstfout = 0 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraints = all-bonds ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = anisotropic ; anisotropic pressure coupling tau_p = 10 compressibility = 0 0 4.5e-5 0 0 0 ; since octanol tries to separate from water and shortening xy plane ref_p = 1.0 1.0 1.0 0 0 0 ; Pull code pull= constraint; pull_geometry = distance ; Pull along the vector connecting the two groups. Components can be selected with pull_dim. pull_dim= N N Y ; put potential only to axis z pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 ; one group to pull pull_group0 = OCT ; reference group (can be empty to set it to 0,0,0) pull_group1 = DRG pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns = 10 m per s pull_k1 = 2000 ; kJ mol^-1 nm^-2 however when I list pull-x.xvg I obtain: @ s0 legend 0 Z @ s1 legend 1 dZ 0. 6.06871 -2.81855 0.0200 6.07793 -2.81861 0.0400 6.08787 -2.81856 0.0600 6.08462 -2.81855 0.0800 6.10028 -2.82007 The situation is even more strange when almost the same mdp with DOPC membrane works fine as can be seen in pull-x.xvg: 0. 3.72735 -1.60929 0.0200 3.72727 -1.60929 0.0400 3.7272 -1.60929 0.0600 3.72716 -1.60929 0.0800 3.72715 -1.60929 0.1000 3.72717 -1.60929 Differences in the working case in mdp are only this: compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 pull_group0 = DOPC Strangerly enough - the same happens in GMX4.0.7 and in GMX4.5.3 I wonder where the difference is, as both logs states that Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 6912 atoms, mass 100624.859 Pull group 1:15 atoms, mass 194.194 Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 9570 atoms, mass 124631.453 Pull group 1:15 atoms, mass 146.146 Where should I look and repair? Thank you in advance Karel Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz -- 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] strange vdw energy from rerun with GBSA model.
Dear Mark Could you please help me out? I can send you the trajectory (1000 snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3. I checked the pdb file in UCSF Chimera and didn't find any crash. I have about 10 snapshot that has high vdw energy. best, dawei On Wed, Aug 10, 2011 at 11:32 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 1:18 AM, Da-Wei Li wrote: Dear Mark That is my thought too.To test this possibility, I created a mdp file without PBC and use trjconv -pbc nojump to make whole protein. From visualization in UCSF Chimera, the trajectory looks fine. But I still have some snapshot that have very high vdw energy. If all you've done is strip water, make molecules whole with trjconv -nojump from a reference configuration that had whole molecules, and use pbc = no in the .mdp file, then that sounds impossible. Mark best dawei On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 12:29 AM, Da-Wei Li wrote: Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high ( 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol. Something is badly wrong - perhaps your treatment of periodicity in the rerun - but we don't have anywhere near enough information to know. It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected. I believe fitting or no-jump processing shall not change the energy at all. Any one has idea about this? As above. 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 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] Constraints not working in pull code (sometimes, sometimes not)
Krapnik wrote: Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 nsteps = 5125000 ; 10.250 ns nstcomm = 1 comm_mode = Linear ; Output parameters nstxout = 0 ; every 1 ns nstvout = 0 nstfout = 0 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraints = all-bonds ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = anisotropic ; anisotropic pressure coupling tau_p = 10 compressibility = 0 0 4.5e-5 0 0 0 ; since octanol tries to separate from water and shortening xy plane ref_p = 1.0 1.0 1.0 0 0 0 ; Pull code pull= constraint; pull_geometry = distance ; Pull along the vector connecting the two groups. Components can be selected with pull_dim. pull_dim= N N Y ; put potential only to axis z pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 ; one group to pull pull_group0 = OCT ; reference group (can be empty to set it to 0,0,0) pull_group1 = DRG pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns = 10 m per s pull_k1 = 2000 ; kJ mol^-1 nm^-2 however when I list pull-x.xvg I obtain: @ s0 legend 0 Z @ s1 legend 1 dZ 0. 6.06871 -2.81855 0.0200 6.07793 -2.81861 0.0400 6.08787 -2.81856 0.0600 6.08462 -2.81855 0.0800 6.10028 -2.82007 The situation is even more strange when almost the same mdp with DOPC membrane works fine as can be seen in pull-x.xvg: 0. 3.72735 -1.60929 0.0200 3.72727 -1.60929 0.0400 3.7272 -1.60929 0.0600 3.72716 -1.60929 0.0800 3.72715 -1.60929 0.1000 3.72717 -1.60929 Differences in the working case in mdp are only this: compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 pull_group0 = DOPC Strangerly enough - the same happens in GMX4.0.7 and in GMX4.5.3 I wonder where the difference is, as both logs states that Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 6912 atoms, mass 100624.859 Pull group 1:15 atoms, mass 194.194 Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 9570 atoms, mass 124631.453 Pull group 1:15 atoms, mass 146.146 Where should I look and repair? I don't see any real problem here. The DOPC membrane probably holds its shape better than the octanol slab and thus the reference position (which determines the constraint) is less mobile. As such, the constraint is more stable in DOPC than in octanol. The slight bump in the octanol system amounts to a change of 0.16%, which I'd say is quite small. You're also looking at the first few frames of the simulation, which may amount to equilibration, but you haven't mentioned if you've done anything prior to this run. As long as there is no systematic change in position, I'd say there's no problem. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Constraints not working in pull code (sometimes, sometimes not)
I agree that Justin is probably correct, although constraints should technically work just fine with a highly dynamic reference group. Any problems should show up as the system blowing up, but not in correctly setting the position. I think that the problems can arise, however, when you have multiple competing constraints. You might, for example, try without constraining the octane bonds -- I think that you should get perfect match in that case. Also, it is worth comparing in single and double precision. Still, I am not sure that you actually did a proper comparison for the following 2 reasons: 1. you have apparently different masses for the pulled group: Pull group 1:15 atoms, mass 194.194 Pull group 1:15 atoms, mass 146.146 2. you used very different starting depth offsets: -2.81855 is not very close to -1.60929 PS: I would personally prefer if you avoided jumping directly to a bug report unless you are sure of it. There is always at least the possibility that you are not using the code correctly. Chris. Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 nsteps = 5125000 ; 10.250 ns nstcomm = 1 comm_mode = Linear ; Output parameters nstxout = 0 ; every 1 ns nstvout = 0 nstfout = 0 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraints = all-bonds ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = anisotropic ; anisotropic pressure coupling tau_p = 10 compressibility = 0 0 4.5e-5 0 0 0 ; since octanol tries to separate from water and shortening xy plane ref_p = 1.0 1.0 1.0 0 0 0 ; Pull code pull= constraint; pull_geometry = distance ; Pull along the vector connecting the two groups. Components can be selected with pull_dim. pull_dim= N N Y ; put potential only to axis z pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 ; one group to pull pull_group0 = OCT ; reference group (can be empty to set it to 0,0,0) pull_group1 = DRG pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns = 10 m per s pull_k1 = 2000 ; kJ mol^-1 nm^-2 however when I list pull-x.xvg I obtain: @ s0 legend 0 Z @ s1 legend 1 dZ 0. 6.06871 -2.81855 0.0200 6.07793 -2.81861 0.0400 6.08787 -2.81856 0.0600 6.08462 -2.81855 0.0800 6.10028 -2.82007 The situation is even more strange when almost the same mdp with DOPC membrane works fine as can be seen in pull-x.xvg: 0. 3.72735 -1.60929 0.0200 3.72727 -1.60929 0.0400 3.7272 -1.60929 0.0600 3.72716 -1.60929 0.0800 3.72715 -1.60929 0.1000 3.72717 -1.60929 Differences in the working case in mdp are only this: compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 pull_group0 = DOPC Strangerly enough - the same happens in GMX4.0.7 and in GMX4.5.3 I wonder where the difference is, as both logs states that Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 6912 atoms, mass 100624.859 Pull group 1:15 atoms, mass 194.194 Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 9570 atoms, mass 124631.453 Pull group 1:15 atoms, mass 146.146 Where should I look and repair? Thank you in advance Karel -- 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] append files in Gromacs 3.3
Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I need to extend them. I have tried to use the option append like in Gromacs 4.0, using: mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append but it does not work, the output files are not appended to the first ones. Do you know how could append files in Gromacs 3.3? Thanks a lot for your help in advance. Best wishes, Rebeca. Dr.Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain -- 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] append files in Gromacs 3.3
Rebeca García Fandiño wrote: Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I need to extend them. I have tried to use the option append like in Gromacs 4.0, using: mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append but it does not work, the output files are not appended to the first ones. Right, because the -append option was added in version 4.0. Do you know how could append files in Gromacs 3.3? Text files can be appended with standard Unix utilities like 'cat' while other Gromacs output files can be appended with other Gromacs utilities (trjcat for trajectories, eneconv for energy files). -Justin Thanks a lot for your help in advance. Best wishes, Rebeca. Dr.Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] append files in Gromacs 3.3
Thanks a lot for your quick answer! Best wishes, Rebeca. Date: Wed, 10 Aug 2011 14:34:42 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] append files in Gromacs 3.3 Rebeca García Fandiño wrote: Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I need to extend them. I have tried to use the option append like in Gromacs 4.0, using: mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append but it does not work, the output files are not appended to the first ones. Right, because the -append option was added in version 4.0. Do you know how could append files in Gromacs 3.3? Text files can be appended with standard Unix utilities like 'cat' while other Gromacs output files can be appended with other Gromacs utilities (trjcat for trajectories, eneconv for energy files). -Justin Thanks a lot for your help in advance. Best wishes, Rebeca. Dr.Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] running at higher temperatures
Hi, When running simulations at a constant higher temperatures (such as simulating a thermophile) would changing ref_t and gen_temp to the appropriate kelvin is enough? Thanks and Regards, Raghu -- 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] Trouble installing mdrun-gpu from gromacs 4.5.4 package
Hello,After undergoing a fresh installation of Gromacs 4.5.4, I still can't seem to get the mdrun-gpu program to compile and install. In order to get the original package to install I had to use the standard automake method (cmake kept getting stuck at the 'make' phase).I have managed to get an older binary version of the mdrun-gpu working correctly, but I would like to not have two different of versions of gromacs floating around my office.The current output from the cmake gives:cmake ../ -DGMX_OPENMM=ON -DGMX_THREADS=OFF-- Using default binary suffix: -gpu-- Using default library suffix: _gpu-- checking for module 'libxml-2.0'-- package 'libxml-2.0' not found-- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)CMake Error at /usr/share/cmake-2.6/Modules/FindPackageHandleStandardArgs.cmake:57 (MESSAGE): Could NOT find CUDA (missing: CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)Call Stack (most recent call first): cmake/FindCUDA.cmake:690 (find_package_handle_standard_args) CMakeLists.txt:434 (find_package)---Any ideas on a fix? Also, does anyone knows of a means to compile mdrun-gpu using the standard automake method?Thanks in advance.Smitty -- 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] running at higher temperatures
Yes, that will be enough. Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ragothaman Yennamalli [ragotha...@gmail.com] Sent: 10 August 2011 20:35 To: Discussion list for GROMACS users Subject: [gmx-users] running at higher temperatures Hi, When running simulations at a constant higher temperatures (such as simulating a thermophile) would changing ref_t and gen_temp to the appropriate kelvin is enough? Thanks and Regards, Raghu -- 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] Viscosity calculations
Dear Gromacs Users, I am trying to learn viscosity calculations using non-equilibrium method in Gromacs 4.5.4. I have gone through Hess paper and several posts on viscosity calculation. I have setup a system of pure water (32000 molecules) and run till 10 ns using NPT and setting cos-acceleration=0.1 nm/ps^2 in .mdp file. Then, I have used following command to get viscosity from energy file. g_energy_d -f .edr -s .tpr -o energy.xvg and selected 1/viscosity from one of the options and I get, Energy Average Err.Est. RMSD Tot-Drift --- 1/Viscosity 1.64374 0.0016 0.0341615 0.00789197 (m s/kg) This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP I have some doubts regarding this result: 1) Can anyone please tell me what are the units of viscosity here. It shows from screen output (as well from energy.xvg) that 1/viscosity is in m-s/kg units. But, the experimental value for pure water is 0.854 cP =0.000854 kg/m-s. So, I have a doubt regarding units coming from GROMACS it is in cP or kg/m-s as printed. If kg/ms are the units then, this value of viscosity for pure water is not correct ? Please tell me what I am doing wrong here. 2) Is this a right way of calculating viscosity using NEMD or I should do it by using 2CosZ*Vel-X option. Please tell me how can I get viscosity from this term. Thanks and Regards, Dr. Rini Gupta UBC, Vancouver -- 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] Recommended parameters for NVE simulation of SPCE water
1. NOTE 1 above suggests that I use vdwtype = Shift. When I do this, do you recommend that I apply long range dispersion corrections for both energy and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr = Ener? Typically, for various (non-NVE) calculations, I have been using DispCorr = no, but I am not sure if this is a good idea. Pages 97-98 of the Gromacs 4.5.4 manual seem to suggest that the energy correction due to DispCorr is small and usually only significant for free energy calculations (which I will not be doing here). As a rule of thumb, do you typically turn dispersion corrections off? For constant pressure simulations, or for reaching the constant pressure equilibrium simulation, you should definitely include a dispersion correction -- the density will be too large, and will be cutoff dependent. For constant volume simulations, the dispersion correction will be constant. It will thus NOT affect energy conservation, but WILL affect average potential energy and average total energy, significantly. 2. NOTE 2 above suggests that I use either coulombtype = PME-Switch or coulombtype = Reaction-Field-zero. Do you have any advice or recommendation? For pretty good energy conservation, I would suggest: rlist = 1.3 coulombtype = PME rcoulomb= 1.1 vdw-type= Switch rvdw-switch= 1.0 rvdw = 1.1 This should work quite well -- you might get some drift after 1-2 ns, but not much. I'm working on developing suggested PME parameters right now for highly quantitative work, but it's not quite ready yet. Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- 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] Kinetic energy of a single molecule
Hi there, I'm trying to find the kinetic energy for a single molecule in the system. I generated one individual group for the molecule in index.ndx file, and also put energygrps = ** (** is the name of the group represented the single molecule) in the .mdp file. But g_energy only allowed me to produce the total kinetic energy of the whole system. For the singe molecule, there were only LJ, Coulomb and T options. Is there any method to generate the kinetic energy just for the single molecule? Many thanks, Size Zheng-- 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] Kinetic energy of a single molecule
Size Zheng wrote: Hi there, I'm trying to find the kinetic energy for a single molecule in the system. I generated one individual group for the molecule in index.ndx file, and also put energygrps = ** (** is the name of the group represented the single molecule) in the .mdp file. But g_energy only allowed me to produce the total kinetic energy of the whole system. For the singe molecule, there were only LJ, Coulomb and T options. Is there any method to generate the kinetic energy just for the single molecule? You can extract rotational and translational KE using g_traj. You can also extract velocity information, from which calculating KE is trivial. This assumes, of course, that you saved velocities in the .trr file. -Justin Many thanks, Size Zheng-- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] To modify PRODRG-generated .itp file?
Hi all, In addition to modifying atomic charges to the .itp file generated by PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4 LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ interactions) with the vdw C12 and C6 parameters I prefer. So should I just make changes to the [ pairs ] section of the .itp file? For example, change ; ai aj fuc0, c1, ... 1 4 1 to ; ai aj fuc0, c1, ... 1 4 1 0.004724 1.84e-6 How can I make sure it will override the parameters in the [ pairtypes ] section of the ffnonbonded.itp file? And I should make these values (c0 for C6, c1 for C12) in accordance with the units in [ pairtypes ] section, right? Moreover, I want to change some dihedral parameters. But I saw the .itp file generated by PRODRG as something like [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 10 5 4 3 1 0.05.9 3 0.05.9 3 so 0.0 is the phase shift, 5.9 is the force constant, 3 is the multiplicity, but why these values appeared twice in a row? When I modify them, should I also write them twice as this format? Will it override dihedral parameters that are already in the ffbonded.itp file? Thanks very much, Yun -- 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] To modify PRODRG-generated .itp file?
Yun Shi wrote: Hi all, In addition to modifying atomic charges to the .itp file generated by PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4 LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ interactions) with the vdw C12 and C6 parameters I prefer. So should I just make changes to the [ pairs ] section of the .itp file? For example, change ; ai aj fuc0, c1, ... 1 4 1 to ; ai aj fuc0, c1, ... 1 4 1 0.004724 1.84e-6 How can I make sure it will override the parameters in the [ pairtypes ] section of the ffnonbonded.itp file? And I should make these values (c0 You can always verify the contents of the topology using gmxdump on the .tpr file produced from it. for C6, c1 for C12) in accordance with the units in [ pairtypes ] section, right? Yes, use correct units. Moreover, I want to change some dihedral parameters. But I saw the .itp file generated by PRODRG as something like [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 10 5 4 3 1 0.05.9 3 0.05.9 3 so 0.0 is the phase shift, 5.9 is the force constant, 3 is the multiplicity, but why these values appeared twice in a row? When I When two sets of values are present, they correspond to the A state and B state for free energy calculations. If you're not doing anything with the free energy code, the second set is ignored. modify them, should I also write them twice as this format? Will it override dihedral parameters that are already in the ffbonded.itp file? It should, yes. But again, use gmxdump to be sure you're getting what you think you should be. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Selenomethionine in pdb file
Hello Friends, I would like to do simulation of a protein containing 'selenomethionine' [MSE] in coordinate file, during the first step of pdb2gmx this residue is not recognizing by any of the force field and getting fatal error 'Residue 'MSE' not found in residue topology database'. Please help me to rectify this problem tahnks. regards vidya -- 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] У вас новое сообщение на Badoo! Посмотреть его сейчас...
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