[gmx-users] Enthalpy and energy questions on a solvated protein

in the event the results I'm getting are really senseless??? Thanks a lot. Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation

[gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

be important ... Thank you very much. Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and Physics of Complex Systems (BIFI

[gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

ft-Verlet? Any suggestion there, please? Thanks a lot. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-February/111037.html Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009

[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

of my trajectories and then paste them again in a new one with trjcat. Finally mdrun -rerun on the new trr and g_energy et Voîla!!! Thank you again Mark, hopefully someone with good programming skills want to develop this functionality in trjorder on ahead. It would be really useful!!! Juan José

[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

anallysis. Could you suggest to me any solutions... Wouldn't be useful to add that functionality to TRJORDER program? Would it be? Thank you very much in advance. Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro

[gmx-users] NORMAL MODES analysis to compute specific heats

On 3/20/17 9:34 AM, Juan José Galano Frutos wrote: >* Hi there: *>>* I've been googled a bit about this issue ( *>* http://thread.gmane.org/gmane.science.biology.gromacs.user/49139, <http://thread.gmane.org/gmane.science.biology.gromacs.user/49139,> *>* http://www.gromacs.org/

[gmx-users] Restraining Protein-ligand distance

that? In the case I need to do a hybrid system what would be a good procedure? Thank you very much. Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute

Re: [gmx-users] Restraining Protein-ligand distance

> > On 3/27/17 8:42 AM, Juan Jos? Galano Frutos wrote: > > Hi there, > > > > I am trying AFEC simulations in complex (ligand-protein), but sometimes I > > get the ligands out the binding site, but I dont want that scenary. I was > > thinking the situation of applying distance retraints between a

[gmx-users] NORMAL MODES analysis to compute specific heats

Sorry for insisting, but has no-one any idea of this? Thanks Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

On 3/17/17 10:35 AM, Juan José Galano Frutos wrote: >* Thank you Justin for your replay. I've read that to compute specific *>* heats (Cv or Cp) it is necessary calculating quantum correction (using *>* the tool g_nmeig). *>* Then, this tool calculates such a correction using the He

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered.

ogy file -mn membed.ndx Input, Opt. Index file Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and Physics of Complex

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

mdrun is not producing the indicated Hessian matrix as set up in the command line. What I am missing, maybe in the .mdp file?? Thank On 3/17/17 8:20 AM, Juan José Galano Frutos wrote: >* Hi there: *>>* I am trying to calculate the specific heat (Cp) of my protein, but I should

[gmx-users] Parameterization of FAD (FLAVIN-ADENINE DINUCLEOTIDE)

elsewhere... Thank you in advance for any help. Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and Physics of Complex Systems

[gmx-users] Hydroxyl bonds rotating too much

the cofactor itself or comes from other issue. I'll post here the result of this test whatever it is. Thank you again. Best On 5/16/17 7:03 AM, Juan José Galano Frutos wrote: >* Hi there: *>>* I am simulating a protein which include as a cofactor a molecule bearing *>* some hyd

[gmx-users] Hydroxyl bonds rotating too much

= all-bonds lincs-warnangle = 60 disre= simple Thank you in advance Best regards Juan José 2017-05-16 13:03 GMT+02:00 Juan José Galano Frutos <juanj...@gmail.com>: > Hi there: > > I am simulating a protein which include as a cofactor a molecule

[gmx-users] Hydroxyl bonds rotating too much

step and afterward to relaunch the equilibration step, but again the same happened. I also checked the topology file of this cofactor but all seems to be fine, I mean charges. Then, what could be happening? Is it common this behaviour in hydroxyl groups?Any help please Thanks Best Juan José

[gmx-users] Issues using Implicit Solvent with Charmm 27

this combination is used but using NAMD. Any help or advise would be appreciated so much. Thank you!! Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06