[gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao)

Did you run also your QM subsystem with the stand-alone version of Orca? 6. ORCA and dummy atom in the gromacs (xi zhao) Gerrit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppo

Re: [gmx-users] CygWin and Gromacs 4.5.5

On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham wrote: > On 8/11/2011 11:35 PM, Szilárd Páll wrote: > > Additionally, AFAIK you will get better performance if you compile > > with MSVC which should be fairly easy if you use CMake - I'm not > > entirely sure about this > > I'd be surprised. Why should

[gmx-users] ORCA and dummy atom in the gromacs

According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns " Back

Re: [gmx-users] newbie question about GROMACS input files

On 9/11/2011 10:08 AM, Markus K. Dahlgren wrote: Hi all! I am new to the Gromacs mailing list and just started looking into Gromacs for MD simulations. I have been working on converting BOSS output into automatic NAMD input for small molecule ligands and now want to create a similar program for

Re: [gmx-users] newbie question about GROMACS input files

Markus K. Dahlgren wrote: Hi all! I am new to the Gromacs mailing list and just started looking into Gromacs for MD simulations. I have been working on converting BOSS output into automatic NAMD input for small molecule ligands and now want to create a similar program for Gromacs input. I have

[gmx-users] newbie question about GROMACS input files

Hi all! I am new to the Gromacs mailing list and just started looking into Gromacs for MD simulations. I have been working on converting BOSS output into automatic NAMD input for small molecule ligands and now want to create a similar program for Gromacs input. I have a question regarding the inpu

Re: [gmx-users] CygWin and Gromacs 4.5.5

On 8/11/2011 11:35 PM, Szilárd Páll wrote: Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Actually I don't think this issue has been addressed. Some NUMA-aware thread_mpi stuff does not work under Cygwin, and code

Re: [gmx-users] where is Coul-LR?

Yun Shi wrote: Hello all, I understand that setting rcoulomb > rlist should give me Coul-LR from the .edr file. But I set rcoulomb = rlist since PME was used to calculate long range electrostatic interactions, and when I tried g_energy, I only have: 58 Coul-SR:Protein-LIG

[gmx-users] where is Coul-LR?

Hello all, I understand that setting rcoulomb > rlist should give me Coul-LR from the .edr file. But I set rcoulomb = rlist since PME was used to calculate long range electrostatic interactions, and when I tried g_energy, I only have: 58 Coul-SR:Protein-LIG 59 LJ-SR:Protein-LIG

Re: [gmx-users] A question about deuteriu order parameters graph

Dear Javier Here is mdp file for MD run title        = cxcr7-DPPC Production MD ; Run parameters integrator    = md        ; leap-frog integrator nsteps        = 50    ; 2 * 50 = 1000 ps (1 ns) dt            = 0.002        ; 2 fs ; Output control nstxout        = 1000        ; save

Re: [gmx-users] CygWin and Gromacs 4.5.5

I have read and have carried out the instruction on the given page. The error arises again. Igor В письме от Втр, 08 Ноя 2011, 16:35 Szilárd Páll пишет: > Hi, > > > There have been quite some discussion on the topic of GROMACS on > Cygwin so please search the mailing list for information. > > >

Re: [gmx-users] barostat for gases

The ideal gas result is -(1/V)(dV/dp)_T = 1/p , so I suppose the value should be = 1.0 bar-1 under standard conditions Krzysztof On 11/8/11 10:51 AM, Dr. Vitaly V. Chaban wrote: Could anybody please suggest a convenient compressibility value for MD boxes of gases (at normal conditions)? Than

Re: [gmx-users] mdp file problem

madhumita das wrote: Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want Probably. Parameterizing such a species pro

Re: [gmx-users] mdp file problem

Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want to also know can I use amber forcefield in GROMACS for pdb files of lipid?

[gmx-users] barostat for gases

Could anybody please suggest a convenient compressibility value for MD boxes of gases (at normal conditions)? Thanks. -- 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@grom

Re: [gmx-users] how to do remd with different tabulated potentials

On 8/11/2011 11:23 PM, ?? wrote: dear teacher, if i want to do remd with different tabulated potentials. how can i use the mdrun's -table (-table table.xvg -tableb table.xvg )? if it can also use like that,there is another question: and how can i rename the tables name ( table_CR1_CR1: i ren

Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns " Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF

Re: [gmx-users] CygWin and Gromacs 4.5.5

Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity a

Re: [gmx-users] mdp file problem

madhumita das wrote: Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , foll

[gmx-users] how to do remd with different tabulated potentials

dear teacher, if i want to do remd with different tabulated potentials. how can i use the mdrun's -table (-table table.xvg -tableb table.xvg )? if it can also use like that,there is another question: and how can i rename the tables name ( table_CR1_CR1: i rename them table_CR1_CR10,table_CR1_C

[gmx-users] CygWin and Gromacs 4.5.5

Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command "make" I receive the error report: numa_malloc.c:117: error: expected '> ' before ' Processor' numa_malloc.c:117: error: expected '> ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' a

[gmx-users] restart the mdrun with the checkpoint file

Dear all, I am trying to use the checkpoint file for the MDrun which war crashed. However, the following error file was obtained in my log file: Reading file md_0_2.tpr, VERSION 4.5.5 (single precision) Reading checkpoint file state.cpt generated: Tue Nov 8 08:06:42 2011 starting mdrun 'Prot

[gmx-users] mdp file problem

Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , following error comes. Steepest D

Re: [gmx-users] Re: PBC - Protein - ligand

Thank you Justin, Mark and Tsjerk. I used the following workflow trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol trjconv -s md.tpr -f pbc_fix.xtc -n index.ndx -pbc cluster -o pbcfixcluster.xtc (Protein+ligand group) trjconv -s md.tpr -f pbcfixcluster.xtc -o center.xtc -center (center on t

Re: [gmx-users] Re: PBC - Protein - ligand

On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Tsjerk, >> >> Thank you. Unfortunately my ligand is not with protein. I put my ligand >> around my protein (in water) running separate simulations to see where can >> it bind. It is close to protein but no

Re: [gmx-users] A question about deuteriu order parameters graph

Hi Alex Deuterium order parameter is a property related to the relative orientation of molecular axis taking the bilayer normal as reference. How to use them to extract useful structural information is a matter of how you interpret the values regarding their definition (see e.g. Egberts and B

Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

I am not sure I understand exactly what you mean but this is all covered in Gerrit's QM/MM tutorials, I'd recommend you go through those. In the ORCA files there is no need to do anything with LAs, GMX will hand a file with the QMsubsystem to ORCA which includes the LA as hydrogens in your case

Re:Re: [gmx-users] remd with different potential at different temperature

dear teacher, if i want to do remd with different tabulated potentials. how can i use the mdrun's -table (-table table.xvg -tableb table.xvg )? if it can also use like that,there is another question: and how can i rename the tables name ( table_CR1_CR1: i rename them table_CR1_CR10,table_CR1_CR1