[gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations

ons. Best regards. Carlos -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

Did you try replacing the line cd ${PBS_O_WORKDIR}/ with cd ‘YOUR_CURRENT_PATH’/ ? Maybe as people already pointed out, the variable is not working properly. Maybe this could work. Best, —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

s/day). So overall I'm quite happy with the performance I'm getting now; and honestly, I don't know if at some point I can get the same performance (running 4 jobs) that I'm getting running just one. Best regards, Carlos —————— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi Mark, I tried that before, but unfortunately in that case (removing —gres=gpu:1 and including in each line the -gpu_id flag) for some reason the jobs are run one at a time (one after the other), so I can’t use properly the whole node. —— Carlos Navarro Retamal Bioinformatic Engineering

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

; node or are you trying to strong-scale? > - what are you simulating? > - can you provide log files of the runs? > > Cheers, > > -- > Szilárd > > On Tue, Jul 23, 2019 at 1:34 AM Carlos Navarro > wrote: > > > > No one can give me an idea of what can b

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

No one can give me an idea of what can be happening? Or how I can solve it? Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile E

[gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

t able to use more than 1 gpu per job, so this is my only choice to use properly the whole node. If you need more information please just let me know. Best regards. Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular

[gmx-users] virtual sites for ligands?

Dear gmx-users, Is there a way to create a vsite-H topology of a ligand using gromacs (pdb2gmx)? Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N

Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb

Dear Justin, To use a time step of 4fs(i clicked send by.mistake) On Tue, Jul 9, 2019 at 7:59 AM Carlos Navarro wrote: > Dear Justin, > Thanks for the reply. > I forgot to mention that indeed the reason of using Berger lipids is > because there are united-atom. I'm plannin

Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb

recently https://www.nature.com/articles/s41467-018-03179-y Best regards, Carlos On Tue, Jul 9, 2019 at 1:50 AM Justin Lemkul wrote: > > > On 7/8/19 7:31 PM, Carlos Navarro wrote: > > Dear gmx-users, > > I was wondering if someone can share the Berger parameters for POPC for

[gmx-users] POPC Berger lipids parameters for AMBER99sb

Dear gmx-users, I was wondering if someone can share the Berger parameters for POPC for Amber99sb (and I they can share also a .pdb .gro file will be even better). I found several for gromos, but I need them form AMBER99sb. Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic

Re: [gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells

([intermolecular_interactions]). Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile E: carlos.navarr...@gmail.com or cnava...@utalca.cl On July 2, 2019 at 3

[gmx-users] problem using more than 1 gpu on a single node - Not all bonded interactions have been properly assigned to the domain decomposition cells

~200k atoms node: 40 cores + 40 threads gpu-per-node= 4 nvidia Tesla V100 if you need more info just let me know. Best regards, Carlos -- ------ Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Univers

[gmx-users] question about make_ndx

e properly make_ndx, but I don’t know how to do this. I have tried with echo "r 1 q" | gmx make_ndx, echo "r 1” “q" | gmx make_ndx, and other combinations, but non of them worked. Any ideas? Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Pos

Re: [gmx-users] charmm36m version for gromacs

Dear Justin, I'll take a look at the comments. Thanks for the quick reply. Best, Carlos El mar., 23 oct. 2018 a las 15:17, Justin Lemkul () escribió: > > > On 10/23/18 2:15 PM, Carlos Navarro wrote: > > Dear gromacs users, > > Where can I download the charmm36m version

[gmx-users] charmm36m version for gromacs

help me. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava

[gmx-users] bromide/iodide parameters for charm36

Dear all, Currently, I'm looking for bromide/iodide parameters for charmm36 without luck. Does anyone know where I can find them? Best regards and thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics

[gmx-users] Problems getting Nitrate oplsaa parameters

com/Downloads ) that was able to convert .cms parameters (from maestro/desmond to gromacs), but know the link is not available anymore. Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulati

[gmx-users] gencof - creating inverted double bilayer systems

inverted) or like this: ↓ ↑ Is there a way to do this with gencof solely? If not, what commands do you suggest me to use? Best regards and thanks in advance, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations

[gmx-users] Problems with make_ndx dealing with big systems

to select specifically only the atoms that form chain B in protein ‘2’ with make_ndx? Thanks in advance, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile

Re: [gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

Hi Mark, I’ll look in more detail the literature regarding this situation. Thanks a lot for your reply. Best, Carlos -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca

[gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

Dear gmx users, This is the third time I’m sending this email, but for some reason is not been accepted. I’m trying to set up a system consisting in a protein embebed into a bilayer. The whole system contains approximately ~40 atoms, so to speed up the simulation I'm using virtual sites. I

[gmx-users] Can I used slipids.ff + charmm36.ff to create a system?

ave read some articles were people indeed can combine different forcefield, but sadly I don’t know how to do that. If this is imposible to do, does someone know vsite parameters for POPC that can be use in charmm36? Hope someone can help me. Best regards, Carlos -- Carlos Navarro Retamal Bioinforma

[gmx-users] Can I used slipids.ff + charmm36.ff to create a system?

ave read some articles were people indeed can combine different forcefield, but sadly I don’t know how to do that. If this is imposible to do, does someone know vsite parameters for POPC that can be use in charmm36? Hope someone can help me. Best regards, Carlos -- Carlos Navarro Retamal Bioinforma

[gmx-users] Computational electrophysiology issues with membrane leakage

57 Backbone_copy_&_TM-helices_copy: 3069 atoms Here are the .gro and .mdp files: .gro: https://www.dropbox.com/s/e4j74zff7mn93bg/membrane.double.gro?dl=0 .mdp: https://www.dropbox.com/s/rsoiv5nkao2ut96/membrane.double.mdp?dl=0 If you need more info just let me know. Hope someone can help

[gmx-users] Computational electrophysiology issues with leakage

the .gro and .mdp files: .gro: https://www.dropbox.com/s/e4j74zff7mn93bg/membrane.double.gro?dl=0 .mdp: https://www.dropbox.com/s/rsoiv5nkao2ut96/membrane.double.mdp?dl=0 If you need more info just let me know. Hope someone can help me to find out where the error is Best regards, Carlos

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

the 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

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

. 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...@gmail.com

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

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 Users

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

the 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] gmx distance - COM distance issue

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, Talca, Chile T: (+56) 712201 798 E: carlos.navarr

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] 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

[gmx-users] Insane.py problem

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. Center of Bioinformatics and Molecular

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

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] Coul-SR energy component - CG simulation

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 26

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] 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

[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

? 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 Retamal Bioinformatics Engineering Ph. D (c) Applied

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] 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

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

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 Talca Av

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

) This is 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. D (c

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

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 Simulations. CBSM University

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

these, 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 Talca Av

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] 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] 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] Applying restraints into 'secondary structure' of a Protein

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 Talca

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

regarding the correct use of a second GPU? Kind regards and a happy new year to everyone, 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

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

, 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: 56-71-201 561 Email

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)

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: 56-71-201 561 Email

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)

-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 Center of Bioinformatics and Molecular Simulations (CBSM

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

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 read the documentation you mention on your previous reply (and hopefully i’ll be able to run 2 process simultaneously . Kind regards, Carlos -- Carlos Navarro

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

% of performance, but when i run a new mdrun instance, the performance drop to about ~30% on each each graphic card ( i set a maximum performance mode). Do you think this may be the problem?. and if this IS the issue, is there a way to solve it? Kind regards, Carlos -- Carlos Navarro Retamal

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

DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center

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

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: 56-71-201 798

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

it faithfully, but it's your job to choose it ;-) Mark On Sun, Dec 14, 2014 at 7:41 PM, Carlos Navarro Retamal cnava...@utalca.cl (mailto:cnava...@utalca.cl) wrote: Dear gromacs users, I’mt trying to improve the performance of some CG simulations by using GPU (with cutoff

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

of the 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] 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

/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 Norte 685, Casilla 721, Talca

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

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: 56-71-201 798, Fax: 56-71-201 561

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

) Warning) Unusual bond between residues: 246 (none) and 247 (protein) 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

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

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, Casilla 721, Talca - Chile Teléfono: 56-71-201 798

[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

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

to 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

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 Bioinformatic engineer Ph.D(c

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] 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

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 Simulations (CBSM