Re: [gmx-users] -pbc nojump failure

Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb file > as an input, so the

Re: [gmx-users] QM calculation

Thank you Justin, I want to do QM calculationbefore running equilibration then run the MD simulation by GROMACS. Do you knowwhich software is appropriate and compatible with GROMACS that after QM calculation I can run the rest of simulation? Best, Mohammad. On Thursday, March 31, 2016 3:43

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

What marks means clearly- you should use second equilibrium output file for final mdrun. i.e. posre_nvt Sent from my iPhone > On 31-Mar-2016, at 12:17 am, Mark Abraham wrote: > > Hi, > > The reasoning behind doing equilibration is covered in various tutorials, >

[gmx-users] pdb2gmx & terminal residues

Dear All, When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with force field, it gave me the warning as following, "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction

Re: [gmx-users] Is the any hydrophobic solutions?

On 3/30/16 12:31 PM, Mijiddorj Batsaikhan wrote: Dear gmx users, I would like to simulate a structure of peptide in hydrophobic solution? Please give me advice and suggestions? Thank you. http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation -Justin --

Re: [gmx-users] a fatal error in step mdrun -v -deffnm em

On 3/30/16 8:36 AM, Brett wrote: Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v

Re: [gmx-users] 54a7 force field & pdb2gmx & topology database

On 3/30/16 8:16 AM, Brett wrote: Dear All, When I work with pdb2gmx for force field 54a7, I meet the following "WARNING: Residue 54 named ILE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is

Re: [gmx-users] QM calculation

On 3/30/16 2:17 AM, mohammad r wrote: Hi gromacs users, I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to gromacs tutorial)? Or I should do it by using gromacsitself? By the way QM calculations are not reliant on MM topologies, like those from PRODRG (which

Re: [gmx-users] Using CHARMM36 in GROMACS

On 3/30/16 5:17 PM, Gregory Poon wrote: Hello everyone, I am learning how to perform dynamics on double-stranded DNA sequences using the CHARMM36 FF I downloaded from the MacKerell lab. I have consulted the GROMACS documentation page regarding specific settings in the .mdp file for CHARMM36

Re: [gmx-users] cgenff CTAB

On 3/30/16 4:34 PM, xy21hb wrote: Dear Justin, I fixed the naming problem as you said. Many thanks for your help. However, the Br- ion in the original pdb does not appear in the converted structure. I wonder how I can introduce it to the CHARMM ff in gromacs by changing the ions.itp file.

[gmx-users] -pbc nojump failure

Hi, I am simulating a protein in its unit cell. I use the original .pdb file as an input, so the initial molecule is not fragmented. At the end of the simulation, I generate a .pdb file containing the trajectory of the protein as follows: gmx trjconv -f nvt_water_frozen.trr -s

Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

and also this one: http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/ On 3/31/16, SAKO MIRZAIE wrote: > hi > you can do MD simulation and compute free energy of folding, > individually. for detect the folding frame or structure, use have to > regard to

Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

hi you can do MD simulation and compute free energy of folding, individually. for detect the folding frame or structure, use have to regard to RMSD. please look at the following webpage: http://www3.mpibpc.mpg.de/groups/de_groot/compbio2/p8/index.html On 3/31/16, Tushar Ranjan Moharana

[gmx-users] Using CHARMM36 in GROMACS

Hello everyone, I am learning how to perform dynamics on double-stranded DNA sequences using the CHARMM36 FF I downloaded from the MacKerell lab. I have consulted the GROMACS documentation page regarding specific settings in the .mdp file for CHARMM36

Re: [gmx-users] cgenff CTAB

Dear Justin, I fixed the naming problem as you said. Many thanks for your help. However, the Br- ion in the original pdb does not appear in the converted structure. I wonder how I can introduce it to the CHARMM ff in gromacs by changing the ions.itp file. Thanks, Yao At 2016-03-30

Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

Hi SAKO MIRZAIE, Thanks for your reply. But how can we calculate difference in folding free energy by doing 2 separate simulations? Please clarify (at least give some hints or references). Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan

Re: [gmx-users] where are the release notes for versions 5.1.1 and 5.1.2?

Hi, Thanks, done. Mark On Wed, Mar 30, 2016 at 8:50 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Thank you Mark. This is very helpful. > > Perhaps update http://www.gromacs.org/About_Gromacs/Release_Notes when > somebody gets a chance. I got to that site via >

Re: [gmx-users] where are the release notes for versions 5.1.1 and 5.1.2?

Thank you Mark. This is very helpful. Perhaps update http://www.gromacs.org/About_Gromacs/Release_Notes when somebody gets a chance. I got to that site via http://www.gromacs.org/Downloads , which is what google suggests when I search download gromacs. Chris.

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

Hi, The reasoning behind doing equilibration is covered in various tutorials, which might be good background for you for other things too. There's no point doing a second equilibration phase if you are going to start production MD from the end point of the first equilibration phase. That's pure

[gmx-users] Number of simulated annealing points

Hi, I'm currently simulating bilayer systems, where our equilibration scheme involves randomly adjusting the temperature to values within a given range. The temperatures can be predetermined, so the we can use the simulated annealing module within GROMACS. However, the maximum number of allowed

Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

you can use of swisspdbviewer, discovery studio or any other softer to do mutation of pdb file. then do MD simulation as a separate protein. On 3/30/16, Tushar Ranjan Moharana wrote: > Hi Everyone, > > I want to find the change in delta G between a protein and its

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

Sorry I didn't get you ...can you please explain me in details On 30-Mar-2016 11:44 pm, "Mark Abraham" wrote: > Hi, > > Why would you do some equilibration, then some further equilibration, and > then start from the point before the further equilibration? > > Mark > >

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

Hi, Why would you do some equilibration, then some further equilibration, and then start from the point before the further equilibration? Mark On Wed, Mar 30, 2016 at 8:12 PM Pradip Kaur wrote: > but i have one question when i m running md.mdp which file should i

Re: [gmx-users] where are the release notes for versions 5.1.1 and 5.1.2?

Hi, See http://manual.gromacs.org/documentation/. Mark On Wed, Mar 30, 2016 at 7:42 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > > I find release notes for gromacs 5.1 here: > http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html . The > text on

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

but i have one question when i m running md.mdp which file should i use as input file ,posre_npt.pdb or posre_nvt.pdb ? On 30 March 2016 at 23:40, Pradip Kaur wrote: > thanks so much > > On 30 March 2016 at 21:33, Mark Abraham wrote: > >>

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

thanks so much On 30 March 2016 at 21:33, Mark Abraham wrote: > Hi, > > The purpose of these equilibration phases is to allow the system to relax > to the desired temperature and pressure. Since you observed that this > happened before starting your production MD ;-)

[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

Hi Everyone, I want to find the change in delta G between a protein and its mutant (with two amino acid mutation). I know for this I have to use "dual topology approach" as mentioned in the manual section 5.7.4. I still couldn't get how to create such a topology. Is there any direct way (like

Re: [gmx-users] *.pdb file for the Tip4p/ice model

Need it for what? To solvate a solute with genbox or for some other sytem setup needs? Common protocol would be to simply use tip4p.gro and then to equilibrate it with the new tip4p/ice parameters. tip4p.gro is in share/gromacs/top/ Chris. From:

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hey :) -ignh does ignore the hydrogens in the input file. It builds those hydrogens that are specified in the force field. For histidines, the protonation state is determined from the possible hydrogen-bonded network, but it is possible to assign specific states interactively, using the option

[gmx-users] where are the release notes for versions 5.1.1 and 5.1.2?

Dear Users: I find release notes for gromacs 5.1 here: http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html . The text on that site ( "These release notes document the functionality changes that have taken place in GROMACS since version 5.0." ) is kind of vague and I am not

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

Chris, I can suggest two possible tweaks, these won't do miracles, but may give you a bit better performance. * icc is better than gcc at optimizing the naiive free energy kernel code. I observed in the past up to 1.5x faster free energy kernel performance with icc 15 vs gcc 4.9 or so. * The

[gmx-users] Is the any hydrophobic solutions?

Dear gmx users, I would like to simulate a structure of peptide in hydrophobic solution? Please give me advice and suggestions? Thank you. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

i have run posre_npt.mdp first and then posre_nvt.mdp by mistake but now going through gromacs manual i found that posre_nvt.mdp is first run and then posre_npt.mdp, but i have already started md.mdp run with posre_nvt.pdb (which was last generated pdb file after mdrun of posre_nvt.mdp ) there is

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

I think using -ignh does not "remove" hydrogens. Hence, you can use it. Sent from my iPhone > On 30-Mar-2016, at 6:04 pm, rajendra kumar wrote: > > Hi, > > As suggested above, use -ignh to ignore hydrogen atoms. To use a specific > Histidine, you may change residue name HIS

[gmx-users] Umbrella sampling along PCA eigenvector using make_edi

Hi everyone, I want to do umbrella sampling along a PCA eigenvector using 'gmx make_edi'. The eigenvectors of the protein backbone atoms were computed using 'gmx covar'. The command for generating the 'sam.edi' file looks like the following: gmx make_edi -s topol.tpr -f eigenvec.trr -eig

[gmx-users] How to perform Essential dynamics sampling and cosine convergence using Gromacs 5.1

Dear all, I want to perform essential dynamics sampling using Gromacs. I have two structures one in closed and another in open state bound with a Mg ion. I also see the collective motion of the both the forms are in a certain direction based on PCA analysis of md trajectories (closed to open

Re: [gmx-users] a fatal error in step mdrun -v -deffnm em

gmx genion -s ions.tpr -o target_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15 At 2016-03-30 21:38:49, "SAKO MIRZAIE" wrote: >let me see your neutralizing command to produce ions.tpr. > >On 3/30/16, Brett wrote: >> Dear

Re: [gmx-users] a fatal error in step mdrun -v -deffnm em

let me see your neutralizing command to produce ions.tpr. On 3/30/16, Brett wrote: > Dear All, > > After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro > -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c > target_solv_ions.gro -p topol.top -o

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

Hi, Yeah, unfortunately Michael's pretty much right - the free-energy kernel is currently that cousin nobody talks about (or to). It's essentially unchanged since GROMACS 4.0 days, except that the Verlet scheme has some kludge so that it can call the same kernel that the group scheme used to

[gmx-users] a fatal error in step mdrun -v -deffnm em

Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave "Step= 15,

[gmx-users] a fatal error in step mdrun -v -deffnm em

Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave "Step= 15,

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, As suggested above, use -ignh to ignore hydrogen atoms. To use a specific Histidine, you may change residue name HIS to HIP(Amber)/HSP(Charmm)/HISH( ​OPLS​ ) or HID(Amber)/HSD(Charmm)/HISD( ​OPLS​ ) or HIE(Amber)/HSE(Charmm)/HISE( ​OPLS​ ) either in PDB file or interactively through pdb2gmx

[gmx-users] 54a7 force field & pdb2gmx & topology database

Dear All, When I work with pdb2gmx for force field 54a7, I meet the following "WARNING: Residue 54 named ILE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps

[gmx-users] FEP with position restraints

Dear all, I'm trying to calculat the binding free energy for a ligand-protein system. I tried to calculate it without restraints but the ligand moved away from the active site. Thus, now I'm trying it by using position restraints for three ions of the active site and three atoms of the ligand.

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, use -ignh flag in pdb2gmx, or you can use of "swiss pdbviewer" software to correct your pdb. On 3/30/16, bio hpc wrote: > Hi, > > we have created some protein pdb files with Maestro. When we try to un an MD > simulation with gromacs, we get errors like: > >>> Atom HD11

[gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, we have created some protein pdb files with Maestro. When we try to un an MD simulation with gromacs, we get errors like: >> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms I tried to find a solution and it seems that internal gromacs dictionary for hydrogens is

[gmx-users] mmpbsa

Hi, Thanks a lot Rajendra. Your information is helpful. Pairwise interaction scheme ? is not implemented in g_mmpbsa. Therefore, g_mmpbsa cannot be used to calculate interaction energy between two residues. With best regards, ?Rajendra ? On Mon, Mar 28, 2016 at 2:37 PM, Prasanna Dr

[gmx-users] *.pdb file for the Tip4p/ice model

need the *.pdb file of Tip4p/ice model. Please help. Regards, Sheelan S C Phys Chem Div Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory,

[gmx-users] output VdW force and electronic static force

Hi all, I wonder is there any way to output VdW force and electronic static force separately in GROMACS. -- Sincerely, Mr. Meng Zhenyu Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University -- Gromacs Users mailing list *

[gmx-users] QM calculation

Hi gromacs users,   I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve generated the initial coordinate and topology files inamber tools then convert it to gromacs format by using parmed

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

Hi, Chris: I'm pretty sure that it's because the nonbonded free energies are much slower than the standard free energies. You state: > I took a look at gmxlib/nonbonded/nb_free_energy.c in v.5.1.2, but I was > unable to find a function called "gmx_waste_time_here()" and beyond that I > was out