Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

Hi already it is answered. run the gmx distance command to understand the problem. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

Hello all, I was practicing the umbrella sampling tutorial by Dr. Justin Lemkul. In my summary_distances.dat file there is only one column ( the column for centre of mass is missing ). Can anyone say what possible mistakes I must have done. Regards, Amit Behera Dept. of Chemical Engg., IISc,

Re: [gmx-users] Distance restraint and pull code

hi, I included this bond assignment right after [bonds] in the topology. [ bonds ] ; i j func b0 kb 1354 3852 6 0.214000 1390 3852 6 0.214000 1721 3852 6 0.214000 1520 3852 6 0.404000 It seems the type 6 works now,

Re: [gmx-users] minor edits to a .gro file

Plumed has a dumpatoms command (see http://plumed.github.io/doc-v2.1/user-doc/html/_d_u_m_p_a_t_o_m_s.html ). You can create virtual atoms whose position is defined based on existing atoms or groups thereof. Plumed can be used as a stand-alone driver or patched onto gromacs for on-the-fly analysis

Re: [gmx-users] Distance restraint and pull code

On 6/9/16 11:21 AM, Hong Tham wrote: hi Justin, in the manual, the [distance restraint] will add flat-bottom harmonic potential to keep distance between 2 atoms. The low, up1, up2 is corresponds to ro, r1, r2 in the equation 4.83 (manual 5.0.7). I understand if rij < r low, up1 up2, mdrun

Re: [gmx-users] Regarding Electrostatic interaction energy

On 6/9/16 9:04 AM, Sathish Kumar wrote: Hi all, I have calculated electrostatic interaction energy between poly alanine peptide and nanomaterial using columb SR term. The nanomaterial has partial charges and peptide also. But the calculated electrostatic interaction energy with peptide is

Re: [gmx-users] Ring planarity

On 6/9/16 12:16 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, I am working on a Protein-drug interaction problem. The small molecule has a cytosine ring. Based on QM calculations and PDB database, The structure for this ring should be planar. However, doing simulations the the ring is

[gmx-users] minor edits to a .gro file

Hi all, I¹m looking to open a .gro file, add in six hydrogen dummy atoms (I can rename the atom name/type, I just need the correct x, y and z coords) to the end of an amino acid sidechain and save whilst preserving as much of the .gro format as it can. I would normally load the crystal/derived

Re: [gmx-users] minor edits to a .gro file

On 6/9/16 2:40 PM, Nash, Anthony wrote: Hi all, I¹m looking to open a .gro file, add in six hydrogen dummy atoms (I can rename the atom name/type, I just need the correct x, y and z coords) to the end of an amino acid sidechain and save whilst preserving as much of the .gro format as it can.

[gmx-users] Ring planarity

Dear Gromacs users, I am working on a Protein-drug interaction problem. The small molecule has a cytosine ring. Based on QM calculations and PDB database, The structure for this ring should be planar. However, doing simulations the the ring is not completely planar . Besides, the NH2 group on

Re: [gmx-users] Distance restraint and pull code

hi Justin, in the manual, the [distance restraint] will add flat-bottom harmonic potential to keep distance between 2 atoms. The low, up1, up2 is corresponds to ro, r1, r2 in the equation 4.83 (manual 5.0.7). I understand if rij < r low, up1 up2, mdrun will add the harmonic potential, if rij

[gmx-users] Regarding Electrostatic interaction energy

Hi all, I have calculated electrostatic interaction energy between poly alanine peptide and nanomaterial using columb SR term. The nanomaterial has partial charges and peptide also. But the calculated electrostatic interaction energy with peptide is around 0.3 kJ/mol. Is this values are correct?

Re: [gmx-users] Distance restraint and pull code

On 6/9/16 8:54 AM, HongTham wrote: Hi, I have another question. I applied 4 pull codes (3 to keep Zn ion in coordination with 3 HIS, 1 to keep Zn ion in coordination with the ligand). The pull code worked effectively. With the same system, when applying 3 distance restraints (to keep Zn ion in

Re: [gmx-users] Distance restraint and pull code

Hi, I have another question. I applied 4 pull codes (3 to keep Zn ion in coordination with 3 HIS, 1 to keep Zn ion in coordination with the ligand). The pull code worked effectively. With the same system, when applying 3 distance restraints (to keep Zn ion in coordination with 3 HIS) and 1 pull

Re: [gmx-users] installation error gromacs-imd

Thanks Mark... Pada tanggal 9 Jun 2016 18.58, "Mark Abraham" menulis: > Hi, > > Please use a released version of GROMACS and don't smash your OS by running > make with sudo. Then we can consider problems that may arise :-) > > Mark > > On Thu, 9 Jun 2016 11:30 Andrian

Re: [gmx-users] installation error gromacs-imd

Hi, Please use a released version of GROMACS and don't smash your OS by running make with sudo. Then we can consider problems that may arise :-) Mark On Thu, 9 Jun 2016 11:30 Andrian Saputra wrote: > Hi..May be its not a gromacs master.. > But i think there is no

Re: [gmx-users] frame with lowest energy

On 6/8/16 8:37 PM, Sana Saeed wrote: hello gromacs users and experts, i have performed 10ns complex simulation of Protein and ligand-complex, now i need the best conformation for further analysis (alchemical analysis: binding free energy simulations). i want to choose best initial structure

Re: [gmx-users] Paradox in .mdp parameter value between Justin's tutorial and martini's one

On 6/9/16 2:37 AM, khourshaeisha...@mech.sharif.ir wrote: pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Gromacs user Im currently working with Coarse grain martini forcefield, but before that Ive used

Re: [gmx-users] simulation with new force field

On 09/06/16 11:23, Chen Jingzhi wrote: Hi GMX user, If I want to do a simulation with a force field that does not exist in gromacs, such as computing electrostatic interaction in Debye-Huckel form and treating hydrophobic interaction with empirical function, is it possible to do with

Re: [gmx-users] installation error gromacs-imd

Hi..May be its not a gromacs master.. But i think there is no problem with source Pada tanggal 9 Jun 2016 15.48, "Kutzner, Carsten" menulis: > > > On 09 Jun 2016, at 09:33, Andrian Saputra > wrote: > > > > Hi,, > > > > Ya i hve tried to install version

[gmx-users] simulation with new force field

Hi GMX user, If I want to do a simulation with a force field that does not exist in gromacs, such as computing electrostatic interaction in Debye-Huckel form and treating hydrophobic interaction with empirical function, is it possible to do with gromacs? BW Jingzhi -- Gromacs Users

Re: [gmx-users] PCA problems

Still no luck When I tried gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -pbc nojump I get a very strange trajectory and covar does not work with this I have also tried gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -fix transxy -pbc mol -s topol.tpr to generate a continuous

Re: [gmx-users] installation error gromacs-imd

> On 09 Jun 2016, at 09:33, Andrian Saputra wrote: > > Hi,, > > Ya i hve tried to install version 5.0 and all compilation is ok... but i > familiar with version 4.5, 4.6... version 5.0 need some changes in mdp > file... But isn't this the master version of GROMACS that

Re: [gmx-users] installation error gromacs-imd

Hi,, Ya i hve tried to install version 5.0 and all compilation is ok... but i familiar with version 4.5, 4.6... version 5.0 need some changes in mdp file... Do you have idea about the error ?? Thank you Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" menulis: > Hi, > > the

Re: [gmx-users] installation error gromacs-imd

Hi, the error message you see has nothing to do with IMD. Have you tried to install a Gromacs 5.0 or 5.1 or 2016 version? These should all work out of the box with IMD. Best, Carsten > On 09 Jun 2016, at 04:35, Andrian Saputra wrote: > > Dear gromacs users > > i

[gmx-users] Paradox in .mdp parameter value between Justin's tutorial and martini's one

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Gromacs user Im currently working with Coarse grain martini forcefield, but before that Ive used all atom simulation. in the below suggested .mdp file [1] , as

Re: [gmx-users] Saving time of the coordinates for conformational entropy

Hi Tsjerk, Yes, you are right but I was also wondering the comments/suggestions on conformational entropy calculation. > On 8 Jun 2016, at 23:33, Tsjerk Wassenaar wrote: > > Hi Qasim, > > The RMSD is not good for assessing convergence, especially if it goes above > 0.5