Re: [gmx-users] Error No default Proper Dih. types

Dear Justin, thanks a lot. Paolo Il giorno dom 26 apr 2020 alle ore 22:33 Justin Lemkul ha scritto: > > > On 4/26/20 3:53 PM, Paolo Costa wrote: > > Dear Justin, > > > > thanks for your extra description. Very nice! > > Last doubt, which values of "phase" and "pn" should I use for [ > >

[gmx-users] about how to create covar.ndx for dihedral Principal Component Analysis

Dear Gromacs users, I am trying to run a dPCA to select the best conformation from my trajectory. When I follow the steps in gromacs manual I have a question about one of the steps: 3. Make an index file , named as covar.ndx, which

[gmx-users] Atom CA used in that entry is not found in the input file

Hello, I edited a few selenomethionine residues, changing "S" to "SD" and removed the "SE" at the end of the line. I then ran pdb2gmx with Charmm36. I get the following error (not sure why the residue number doesn't match): Fatal error: Residue 324 named GLY of a molecule in the input file was

Re: [gmx-users] Error No default Proper Dih. types

On 4/26/20 3:53 PM, Paolo Costa wrote: Dear Justin, thanks for your extra description. Very nice! Last doubt, which values of "phase" and "pn" should I use for [ dihedraltypes ]? If the force constant is zero, the remaining parameters are irrelevant. -Justin Thanks again. Paolo Il

Re: [gmx-users] Error No default Proper Dih. types

Dear Justin, thanks for your extra description. Very nice! Last doubt, which values of "phase" and "pn" should I use for [ dihedraltypes ]? Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul ha scritto: > > > On 4/26/20 2:08 PM, Paolo Costa wrote: > > Dear Justin, > >

Re: [gmx-users] Error No default Proper Dih. types

On 4/26/20 2:08 PM, Paolo Costa wrote: Dear Justin, thanks a lot for your quick reply and useful information. Thus, I will go through to all the dihedral terms and define zero the corresponding force constant as you suggested. In any case, I guess it will be too much work to calculate also

[gmx-users] wham - Bootstraping

Dear all, Each windows of a wham analysis is a 30 ns long simulation. And I choose 25 ns of them in gmx wham -b 5000 -nBootstrap 250 -bins 250 -bs-method b-hist ... . I noticed the below massages in the log file that only 395 , 1854, and around 2000 are being evaluated out of 24250

Re: [gmx-users] Error No default Proper Dih. types

Dear Justin, thanks a lot for your quick reply and useful information. Thus, I will go through to all the dihedral terms and define zero the corresponding force constant as you suggested. In any case, I guess it will be too much work to calculate also the force constant for the torsion angle

Re: [gmx-users] Error No default Proper Dih. types

On 4/26/20 1:57 PM, Paolo Costa wrote: Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters from known

[gmx-users] Error No default Proper Dih. types

Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters from known works, while the parameters for the bonding

Re: [gmx-users] gromacs installation (2020&2019)

Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same time? If not a couple of things to keep in mind. Be sure before installing Gromacs you have all the utilities that Gromacs use, compilers, etc and that their versions are supported. I saw you are trying to install it for GPU,

Re: [gmx-users] lincs warning

Hi Afsane, You need to provide more details of the simulation, such as how you generated the configuration and topology, what force field you used and so on, or we can not give you any advice. Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip:

Re: [gmx-users] gromacs installation (2020&2019)

Hi Netaly, Although I do not know the exact reason of the failure, after skimming through your command, I think that you probably need to assign absolute path to CMAKE_INSTALL_PREFIX and have access to the internet for downloading REGRESSIONTEST and FFTW package. If you are new to GROMACS, I

Re: [gmx-users] Fatal error pdb2gmx

On 4/26/20 5:15 AM, Paolo Costa wrote: Dear Gromax users, I created a new residue of 118 atoms within Amber99 force field. However when I run the "pdb2gmx" I got many times the following warning: "*WARNING: Duplicate line found in or between hackblock and rtp entries" *and in the end I got

[gmx-users] Fatal error pdb2gmx

Dear Gromax users, I created a new residue of 118 atoms within Amber99 force field. However when I run the "pdb2gmx" I got many times the following warning: "*WARNING: Duplicate line found in or between hackblock and rtp entries" *and in the end I got the following fatal error: "*Atom O10 in

[gmx-users] gromacs installation (2020&2019)

Dear All, I am trying to install gromacs 2020 and 2019 versions on CentOS release 6.10 (Final) linux system. I passed throuht cmake compilation. Using command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=gromacs2020