[gmx-users] RDF analysis with respect to center of mass of Protein

with respect to the glycerol molecules, but i don’t know how to use make_ndx to create such kind of group. Is there a way to do this? Or maybe you may think in a better idea. Hope someone can help me. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied

Re: [gmx-users] RDF analysis with respect to center of mass of rotein

r-o TEST-glycerol.xvg > group 1: Protein group 2: GOL (glycerol molecules) Thanks again for your valuable help, Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simul

Re: [gmx-users] RDF analysis with respect to center of mass of otein

use the second image to show the RDF. Thanks a lot for your valuable help, Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Not at all. I’m using the .xtc file that comes from the simulation. What do you mean with the nrexcl issue? Is there a way i can fix it? -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations

Re: [gmx-users] RDF analysis with respect to center of mass of otein

-o > traj_center.xtc > > > and then i measure the RDF with the following one: > g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o > TEST-carbons.xvg But i’m still seeing these weirds peaks a short distance. Best regards, Carlos -- Carlos Navarro Retamal Bioinfor

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Hi Marcelo, Thanks for your reply. Sadly it didn’t work either, so i’m trying to generate a new .tpr file by changing the nrexcl values just as Justin suggest. Hope this may works. Thanks the two of you. Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied

[gmx-users] FEP residue mutation tutorial

Dear gromacs users, Is there a tutorial/guide or something for beginners to perform FEP for amino acid mutations on gromacs? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and

[gmx-users] Problem - How to center a protein in a CG simulation

mbrane in order to perform the ‘backward’ step to obtain an AA representation of my system and perform a new MD simulation i’m kind of stuck. I don’t know what to do :/ Hope someone can help me. Have a nice week, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied S

Re: [gmx-users] Problem - How to center a protein in a CG simulation

-- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com

Re: [gmx-users] Problem - How to center a protein in a CG simulation

0L31 AA-model http://cl.ly/0U2r2n0F290i Thanks to both of you for all your help, Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Nort

Re: [gmx-users] Problem - How to center a protein in a CG simulation

f the box. What could it be? Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 79

Re: [gmx-users] Problem - How to center a protein in a CG simulation

ein) sorry for asking to much stuffs, but this is my first time trying to convert a system form a CG-representation to an AA one. Thanks for all of your help. Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile

Re: [gmx-users] Problem - How to center a protein in a CG simulation

mphasise that using it will be huge change on the martini ff. Best regards to all of you, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casill

[gmx-users] g_hbond tool question

ns i got different values (higher) than the values got from ‘Protein’ - ‘SOL’ Why is this happening? Am i interpreting in a wrong way what the selection ‘Protein’ - ‘SOL’ is considering? Hope someone can help me. Thanks in advances, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(

Re: [gmx-users] g_hbond tool question

chain EXCEPT the hydrogen atoms. So in that case, with the option ‘sidechain' + 'MainChain+H’ i got the same values that i got with ‘Protein’ (the whole protein) Thanks a lot!, Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Unive

[gmx-users] adding hydrogen atoms into a POPC membrane

hydrogen atoms of the membrane. So, is there a way to add the missing atoms after this step? and if its not posible, could someone provide me with the ‘correct’ *itp file (hopefully gromos or charmm ff) ? Thanks in advance. Have a nice weekend, Carlos -- Carlos Navarro Retamal Bioinformatic

Re: [gmx-users] adding hydrogen atoms into a POPC membrane

Hi everyone, First of all thanks to both of you for your quick replies. Dear Tsjerk, I’ll be much appreciated if you could send me the *itp file of POPC. Thanks a lot, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of

[gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

ll be appreciated for your help. Have a nice day, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-20

Re: [gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

be the best for the vdw term. Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71

Re: [gmx-users] adding hydrogen atoms into a POPC membrane

Dear Tsjerk, Could you please send me the popc.itp file for chamm36 forcefield? If you have any troubles with my institutional email account, try to my gmail account (it is on my signature) Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science

[gmx-users] Converting Amber parameters to gromacs parameters

Dear gromacs users, I found recently some parameters for a thylakoid membrane, but sadly they were for the Amber software. Is there a way to transform them into gromacs parameters? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science

[gmx-users] Installing GTX 980 on linux - which distro should i use?

threads where people discuss their bencharmks (or their opinions) regarding this graphic card, so i want to know: in which linux distro did you installed gromacs in order to work the GTX 980? Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science

Re: [gmx-users] Installing GTX 980 on linux - which distro should i se?

Dear everyone, Thanks a lot for all your help. I tried Mr. Mohammad said without luck (maybe the problem is due i have 2 graphic cards? ), In any case, i’ll try with Scientific linux now.. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science

[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

, in ba > compressibility = 4.5e-5; isothermal compressibilit > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr= EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no; a

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

100.0 > - > > Force evaluation time GPU/CPU: 2.336 ms/2.324 ms = 1.005 > For optimal performance this ratio should be close to 1! > >Core t (s) Wall t (s)(%) >Time:

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

~90k atoms -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

now. Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

Hi Albert, Thanks for your advice. Sorry for asking this, but how can i do this? I mean, use the Nvidia compiler during the gromacs installation? Which flag should i add? Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

tool kit and compile gromacs again. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

nds: > mdrun -deffnm test1 -gpu_id 0 -v > mdrun -deffnm test2 -gpu_id 1 -v Is there a better way to perform multiple md simulations at the same time? Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Cente

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

ava...@utalca.cl On Tuesday, December 30, 2014 at 3:40 PM, Justin Lemkul wrote: > > > On 12/30/14 1:38 PM, Carlos Navarro Retamal wrote: > > Dear Justin, > > Thanks a lot for your reply. > > > > > You can use the multiple cards to run > > > con

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

71-201 561 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl On Tuesday, December 30, 2014 at 4:03 PM, Carlos Navarro Retamal wrote: > Dear Justin, > Thanks a lot for your reply. > I tried with another system (~130k with the same results) 1GPU > 2 GPU’s > In any case i’ll rea

Re: [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

cutoff 1.594: 3571.9 M-cycles > optimal pme grid 84 84 80, coulomb cutoff 1.464 >Step Time Lambda >5000 10.00.0 and when i add the second graphic card the performance drop again to about 5-6ns/day This pe

[gmx-users] Applying restraints into 'secondary structure' of a Protein

cting peripherally with respect to a bilayer membrane), so if you think in something else please feel free to make any suggestions. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of

Re: [gmx-users] Applying restraints into 'secondary structure' of a Protein

performing around ~40ns on system with about 90k - 120k atoms, and this system; POPC+water molecules+protein, is around 110k). Thanks for your help -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca

[gmx-users] regarding glycolipids parameters for GROMACS

Dear gromacs users, I was wondering, are they glycolipids (MGDG more specifically) parameters availably for gromacs package? it doesn’t matter for which forcefield they were constructed. Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center

Re: [gmx-users] regarding glycolipids parameters for GROMACS

As usual thanks a lot Justin, i’ll email you asap, Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr

[gmx-users] System blowing up - equilibration step - CG simulation

avoid this issue? I tried increasing the EM step without luck. If you need more info related my problem please let me know. Hope someone can help me. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulatio

Re: [gmx-users] System blowing up - equilibration step - CG simulation

s the first time i used the parameters gotten from http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp so i don’t know if this kind of molecules requieres an specific temperature (for example) Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph.

Re: [gmx-users] System blowing up - equilibration step - CG simulation

step to 50ns. What else do you suggest me? Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com

Re: [gmx-users] System blowing up - equilibration step - CG simulation

, because in Martini forums all the tutorial are still using gromacs version 4.6.X as the standard. Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca

Re: [gmx-users] System blowing up - equilibration step - CG simulation

of my simulation since i’m not able to use my GPU's (coulomb type and vdw_type = shift). What do you suggest me to do? Thanks in advance, -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Tal

[gmx-users] Best strategy to set up a system for an Umbrella sampling simulations

m a AA simulations, i don’t think that i can use this tool. Probably is a silly question, but i hope someone can help me. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Ta

[gmx-users] gmx mindist issue

-- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- Gromacs Users mailing list * Please

Re: [gmx-users] gmx mindist issue

Nobody know what may be happening? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com

[gmx-users] non-matching atom names in CG simulations

) created by insane script. My question is, it is ok if i just change the order in the *itp file, to make it identical as the one found in the *gro file? If not, what should i do in order to avoid any kind of issue during the simulation?. Thanks in advance Best regards, Carlos -- Carlos Navarro

Re: [gmx-users] non-matching atom names in CG simulations

;), What about the first three lines? Is it order important? Also i’m writing an email to your collaborator about how he used insane to build this mixture membrane (with respect to POPC-MGDG and POPC-SQDG i didn’t have any kind of problems) Thanks a lot Tsjerk. Best, Carlos -- Carlos Navarro Ret

[gmx-users] Coul-SR energy component - CG simulation

about these. By the way, i’m using a shift potential to describe coulomb and vdw interactions (since martini force field was parametriced in that way),do you think that maybe this issue is because i’m not using PME to describe this interaction? Best, Carlos -- Carlos Navarro Retamal

Re: [gmx-users] Coul-SR energy component - CG simulation

6.7 without luck Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl On March

Re: [gmx-users] Coul-SR energy component - CG simulation

to make electrostatic interactions :) (as well as SQDG as you already mentioned it) :) Thanks again. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N

[gmx-users] Insane.py problem

onvert string to float: Is this because i’m using float numbers to describe the specific amount of lipids? If this is the case, can someone suggest me an approach to overcome this issue? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences

Re: [gmx-users] Insane.py problem

Hi Tsjerk Thanks for your reply. I found that the problem was the empty space between the number and the comma. How silly of me. Thanks in any case :) Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM

Re: [gmx-users] Insane.py problem

I have no idea either. with: ./insane.py -f PSII-CG.pdb -pbc square -box 25,20,15 -l CPG:0.5557 -l PPG:0.0543 -l CDGDG:2.56 -l CMGDG:4.35 -l CSQDB:2.4774 -l CSQDG:0.0026 -sol W -o system.gro works perfectly. Best, carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied

[gmx-users] Segmentation fault (core dumped) version 4.6.*

Segmentation fault (core dumped) That is not telling me anything useful :/ I tried also installing the 4.6.3, but sadly i have the same problems with this version. Hope someone can help me. Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of

Re: [gmx-users] Segmentation fault (core dumped) version 4.6.*

-lastenerstring Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. Segmentation fault (core dumped) Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c

[gmx-users] gmx distance - COM distance issue

tance) without luck (i got the same values as before). What could be the reason? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talc

Re: [gmx-users] gmx distance - COM distance issue

adsorption process of the protein into the bilayer. Thanks a lot. Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr

[gmx-users] there are particles with all coordinates zero

tting the same error: -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- Gromacs

[gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

production data. Any thoughts/suggestions are more than welcome. Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr.

Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

doesn’t generate anything (any *xvg file). I don’t know what I’m doing wrong Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E

Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

membrane thickness of a bilayer? Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava