Re: [gmx-users] Dftb as qmmm method with gromacs

f_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > > Hi, > > Instead of the flag to Cmake you could also manually modify CMakeCache.txt > > //QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess, > // orca > GMX_QMMM_PROGRAM:STRING=dftb > > best, >

[gmx-users] Dftb as qmmm method with gromacs

Hello all, I want to use dftb as a qmmm method with gromacs as explained in a recent research article " http://onlinelibrary.wiley.com/doi/10.1002/jcc.24029/abstract;. When I am trying to compile gromacs-5.0 with dftb using flag " *-DGMX_QMMM_DFTB*", the cmake .. command is terminating with the

Re: [gmx-users] addition of hydronium ion in simulation box

-automatic-cleanup?tc_serial=22719463909_rand=310256639_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin

Re: [gmx-users] addition of hydronium ion in simulation box

-automatic-cleanup?tc_serial=22713087415_rand=1639918188_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Sorry, I have posted my reply in wrong thread. On Tuesday, September 22, 2015, Padmani Sandhu <padmanisandh...@gmail.com> wrote: > Hello justin, > > Thanks, actually I want to study movement of protons along the lenght of a > water channel. > > > Regards, > > &

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

-automatic-cleanup?tc_serial=22713052843_rand=144206_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin

[gmx-users] addition of hydronium ion in simulation box

Hello all, How we can hydronium ions in a simulation box... With regards, Padmani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Problem in running CPMD with gmx-3.3.1

Hello all, *I am running CPMD v4.1 in hybrid with gmx-3.3.1_qmmm-1.3.2. While running the qmmm_example ethane_em, the mdrun is evoked CPMD but the process was stopped with an error message without completing energy minimization:* MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

Re: [gmx-users] Error while configuring gmx-3.3.1

/ which is a standard unix command. Mark On Thu, Aug 20, 2015 at 5:52 AM Padmani Sandhu padmanisandh...@gmail.com wrote: Hello Justin, I have copied both the .itp files which were giving error in to /usr/local/gromacs/share/top using command: sudo cp BH4_oplsaa.itp /usr/local

Re: [gmx-users] Error while configuring gmx-3.3.1

. There is no problem with topology, its working fine with gromacs-4.5.6 and later versions. Thanks Padmani On Wed, Aug 19, 2015 at 5:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/15 7:58 AM, Padmani Sandhu wrote: Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled

[gmx-users] Error while configuring gmx-3.3.1

Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using following commands: ./configure make sudo make install *However the program was installed but while running grommp, it was terminated with an error :* checking input for internal consistency... calling

Re: [gmx-users] Error while configuring gmx-3.3.1

that all the files in *gromacs-3.3.1/share/top *can be copied to */usr/local/gromacs/share/top.* Thanks Padmani On Wed, Aug 19, 2015 at 5:42 PM, Padmani Sandhu padmanisandh...@gmail.com wrote: 1. I am using it with CPMD as they have mentioned this version of gromacs only. 2. The top-level

[gmx-users] Proton transfer reaction in gromacs

Hello, I want to study proton transfer reaction in a protein channel using gromacs. I read in the literature that it is not possible to do this by classical MD, then what are the other ways to perform it in gromacs..?? -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology

[gmx-users] Problem in equilibration of POPS lipid bilayer

Hello all, I have generated a mixed lipid bilayer constituting POPS and POPC lipid molecules. I am trying to perform MD simulation but the POPS lipid molecules are tearing apart on energy minimization. Please help me..!! Thanks With regards, Padmani -- -- Gromacs Users mailing list *

Re: [gmx-users] Problem in equilibration of POPS lipid bilayer

://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=21904080572tc_rand=1921652829utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 On 7/8/15 7:57 AM, Padmani Sandhu wrote: Hello all, I have generated a mixed lipid bilayer constituting POPS and POPC lipid molecules

[gmx-users] Problem in energy minimization of Protein-ligand complex in Lipid membrane

Hello everyone, I am trying to energy minimize protein-ligand complex in lipid membrane. I am using LAMBADA script, after extracting Ligand. LAMBADA script do not recognise ligand molecule, after insertion when I am trying to reinsert ligand in to Prot_memb system, it does not bind to protein

[gmx-users] problem in energy minimization of protein in POPC lipid membrane

Hello all, Do we need to create a box using editconf before using grompp to carry out energy minimization between shrinking steps.??? Thanks, Padmani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] lipid molecules are overlapping with proteinmolecule

=384970619utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=19297575572tc_rand=384970619utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 On 11/11/14 10:18 PM, Padmani Sandhu wrote

[gmx-users] lipid molecules are overlapping with protein molecule

, but that is also giving error during grompp. Thanks Padmani, -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India

Re: [gmx-users] lipid molecules are overlapping with proteinmolecule

=19280033379tc_rand=975494227utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 On 11/11/14 6:45 AM, Padmani Sandhu wrote: Hello all, I am trying to energy minimize a trimeric protein in DPPC bilayer but facing problem in reaching desired lipid per area using inflategro.pl

Re: [gmx-users] Unstable system [was: (no subject)]

info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=18953694948tc_rand=2029571302utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 Please remember to use a sensible subject line. On 10/15/14 6:53 AM, Padmani Sandhu wrote: Hello I have energy

Re: [gmx-users] Unstable system [was: (no subject)]

On 10/15/14 12:35 PM, Padmani Sandhu wrote: Hello Justin, Epot = -3.4264112e+07 Fmax= 8.5767386e+02 from energy minimization. Seems reasonable. I am using force field Gromos43a1 and ligand parameters were derived from PRODRG. PRODRG produces topologies full of errors. Have you done

[gmx-users] (no subject)

= 1 comm-mode = Linear comm-grps = Protein_LMT_POPC Water_and_ions Please help me... -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin