Re: [gmx-users] rotacf error

How I can remove the prolines, I have 6 in the protein... Em dom., 15 de dez. de 2019 às 03:10, David van der Spoel < sp...@xray.bmc.uu.se> escreveu: > Den 2019-12-15 kl. 04:13, skrev Mario Andres Rodriguez Pineda: > > Hi all > > I want to calculate the order parameter of t

[gmx-users] rotacf error

. In the attached file I show more details about the error andhow I created the index. Could you help me to correct the index for calculate the correlation time and in turn the order parameter S2? Thanks for your help. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL

Re: [gmx-users] distance analysis error

ty > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On Thu, 17 Oct 2019 at 09:28, Mario Andres Rodriguez Pineda < > mand...@iq.us

[gmx-users] distance analysis error

that i want measure the distance in all MD trajectory: [ F519 ] 1450 [ S678 ] 3976 Can someone help me? Thanks -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av

Re: [gmx-users] dssp error

I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an executable Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao escreveu: > Have a check the installation of DSSP, > did you set the variable DSSP for do_dssp? > > > All the best, > Qinghua > > >

Re: [gmx-users] dssp error

. Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao escreveu: > Hello, > > Just follow the suggestion by adding "-ver 2" to your command. > > > All the best, > Qinghua > > On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: > > Good afternoon.

[gmx-users] dssp error

: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante

[gmx-users] gpu cpu use

for your help . -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- Gromacs Users mailing list

Re: [gmx-users] gromacs error in vacuum preparation simulation

Thanks, for your help. Em seg, 11 de mar de 2019 às 19:31, Justin Lemkul escreveu: > > > On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote: > > If i don't use -maxwarn option they send me the same error. > > Omitting -maxwarn won't fix problems, but it is a very ba

Re: [gmx-users] gromacs error in vacuum preparation simulation

às 17:12, Justin Lemkul escreveu: > > > On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote: > > Hi everybody > > I want to do one dynamic simulation of one protein > > i'm try to minimize the protein in vacum before the simulation runing but >

[gmx-users] gromacs error in vacuum preparation simulation

. -- this is the command that i use for minimization in vacum. gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o cbd212_vac.tpr -maxwarn 1 I can't find the solution for this problem. Thanks for your help -- *MSc. MARIO ANDRÉS

Re: [gmx-users] doubt regarding order parameter calculated by gmx chi S2max and S2min

MX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *MSc. MARI

Re: [gmx-users] Recovery simulation error (Bratin Kumar Das)

t -append -deffnm > cbd211_md > > > > On Sat, Nov 17, 2018, 9:26 AM Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in> > > wrote: > > > > > Use -deffnm flag and specify the name ..same as the previous output > > > file...do not forget to give th

[gmx-users] Recovery simulation error

and write separate new parts. For mere concatenation of files, you should use the gmx trjcat tool instead. I used this command: gmx mdrun -s cbd211_md.tpr -cpi cbd211_md.cpt -v All the archives ar in the directory Can you help me? Thanks -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante

[gmx-users] GPU ERROR RUNING A SIMULATION

for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file. Can you help me please? I don't know what to do in this case and the simulations is very slow... -- *MSc. MARIO ANDRÉS

Re: [gmx-users] simulation error

:36, Justin Lemkul escreveu: > > > On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote: > > These were the errors until the moment of executing the minimization: > > > > After adding ions grompp: > > NOTE 1 [file topol.top, line 37566]: > >Syste

Re: [gmx-users] simulation error

for transmission (in valid comm) Abort (core dumped) In attach send you the mdp archive for minimization run. Thanks for your help Em seg, 17 de set de 2018 às 19:56, Justin Lemkul escreveu: > > > On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote: > > Hi everyone. > >

[gmx-users] simulation error

not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates tMPI error: Receive buffer size too small for transmission (in valid comm) Abort (core dumped) How i can fix it? Thanks for your help. -- *MSc. MARIO ANDRÉS RODRÍGUEZ

Re: [gmx-users] Average data files with gmx analyze

Dear Justin: thank you very much! best regards! Mario Campo > > > On 11/29/17 4:35 AM, ma...@exactas.unlpam.edu.ar wrote: >> Dear GROMACS developers: >> The gmx tutorial tells me that in order to average data from columns of >> several similar files XVG, I must use

[gmx-users] Average data files with gmx analyze

Dear GROMACS developers: The gmx tutorial tells me that in order to average data from columns of several similar files XVG, I must use gmx analize "gmx analyze reads an ASCII file and analyzes data sets. ... Multiple sets can also be read when they are separated by & (option -n); in this case only

Re: [gmx-users] "cmake" failed to install

n_simd_support_not_found) > CMakeLists.txt:648 (gmx_manage_simd) > > > > > -- Configuring incomplete, errors occurred! > See also > "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log". > See also > "/home/lee/Jef/gromacs/gromacs-5.1.

Re: [gmx-users] "cmake" failed to install

Dear Cheng: I solved that problem by following step by step instructions of the next page: https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/ Best Regards Mario Campo Dpto Física - UNLPam La Pampa Argentina > Dear Gromacs, > I did the

Re: [gmx-users] Switching Group to Verlet

Dear Mahmood, I always find very useful this page: http://manual.gromacs.org/online/mdp_opt.html For your particular case I think you should look at http://manual.gromacs.org/online/mdp_opt.html#out Cheers, Mario 2016-10-21 15:33 GMT+01:00 Mahmood Naderan <mahmood...@gmail.com>: >

Re: [gmx-users] mdrun -membed Sorry, parallel g_membed is not yet fully functional.

The simulation comes to an end and it produces some output file indeed. Yet, no .gro file is present in the directory. I guess I'm missing something in the process. 2016-07-22 16:54 GMT+02:00 -Mario <marios9...@gmail.com>: > I confirm that it worked smoothly by adding this command. &g

Re: [gmx-users] mdrun -membed Sorry, parallel g_membed is not yet fully functional.

to be produced, but I can only see .edr and .log. Don't know if I'm getting it wrong or something. Thanks deeply for your help. -Mario 2016-07-21 23:29 GMT+02:00 -Mario <marios9...@gmail.com>: > I'm trying to insert a protein in membrane using the g_membed method, even > though this co

[gmx-users] Implementation of the v-rescale integrator

? Because, in the original formulation in the paper, the value that appears is tau and this should be calculated as (1.0 - factor) instead of as (1.0 - factor)*factor. Thank you very much. Best regards, Mario -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

[gmx-users] Normal mode analysis after equilibration

this trend so my question is to confirm that I am not missing something. Thank you very much. Best, Mario -- 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

Re: [gmx-users] Normal mode analysis after equilibration

Dear David, Thank you very much for your answer. 2016-01-14 20:20 GMT+01:00 David van der Spoel <sp...@xray.bmc.uu.se>: > On 14/01/16 18:23, Mario Fernández Pendás wrote: > >> Dear All, >> >> I am running simulations of a toxin placed in the middle of

Re: [gmx-users] Realistic water simulation

Dear David, Thank you very much for your answer. I am using a flexible version of the model from http://journals.aps.org/prb/abstract/10.1103/PhysRevB.31.2643 Cheers, Mario 2015-11-25 16:16 GMT+01:00 David van der Spoel <sp...@xray.bmc.uu.se>: > On 25/11/15 13:02, Mario Fernánd

[gmx-users] Realistic water simulation

Dear All, Is it realistic to perform simulations of a SPC water system consisting on 864 elements. Should I increase the size? The force field used is OPLS-AA/L. Thank you very much. Best, Mario -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Study of sampling of villin headpiece

. Thank you very much for your suggestions. Best, Mario 2015-07-30 13:51 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: Hi, I do not think it is sensible to attempt to measure the relative efficiency of two different methods in the absence of evidence that either has sampled approximately

[gmx-users] Study of sampling of villin headpiece

you suggest me to see the difference in sampling between my two methods? Thank you very much. Best, Mario -- 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

Re: [gmx-users] (no subject)

Hi, If you want to preserve the cubic shape of your box you need to choose a barostat that allows to use the isotropic option. However, when using a barostat your box size is going to change for sure. Cheers, Mario 2015-06-03 10:06 GMT+02:00 Sotirios Dionysios I. Papadatos si.papada

Re: [gmx-users] Constraints in the villin system

Thank you very much Justin. 2015-06-01 18:10 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 6/1/15 11:55 AM, Mario Fernández Pendás wrote: Dear all, I am interested in simulations with the villin system using the constraint algorithm SHAKE. From the physical point of view, does it make

[gmx-users] Constraints in the villin system

decomposition, the LINCS algorithm is suggested and I am still interested in using SHAKE. Thank you very much. Cheers, Mario -- 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

Re: [gmx-users] check_bonds_timestep() only reports the first suspicious bond

Thank you very much Mark. 2015-02-20 0:19 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Hi, Nothing has happened. Mark On Thu, Feb 19, 2015 at 4:31 PM, Mario Fernández Pendás mariof...@gmail.com wrote: Dear all, How is the situation with this issue? http

[gmx-users] check_bonds_timestep() only reports the first suspicious bond

Dear all, How is the situation with this issue? http://redmine.gromacs.org/issues/667 I am planning to modify this function to look for the fastest oscillations in each system and that is why I am asking this question. Thank you very much. Best regards, Mario -- Gromacs Users mailing list

Re: [gmx-users] Maximun time-step recommended in the grompp part for each system

completely what is the theory behind this check_bonds_timestep() routine. This is why I am asking how it is obtained explicitly that 4.44 number. I hope my question is more clear now. Thank you very much. Best regards, Mario 2014-12-14 2:15 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 12/13/14 11:34

Re: [gmx-users] Maximun time-step recommended in the grompp part for each system

Hi Justin, Thank you very much for your help. I will try to find out how that limit is obtained. But of course any useful reference would be very much appreciated. Thank you. Best regards, Mario 2014-12-15 14:50 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 12/15/14 6:57 AM, Mario Fernández

Re: [gmx-users] Maximun time-step recommended in the grompp part for each system

Some extra information about this topic: We are exicitely interested in NOT using any kind of constraints. As you may assume, the purpose of this study is purely theoretical. Thank you very much. Best regards, Mario El 11/12/2014 18:20, Mario Fernández Pendás mariof...@gmail.com escribió

[gmx-users] Maximun time-step recommended in the grompp part for each system

Am I right? I have also found an issue in redmine for the function check_bonds_timestep() reporting that it only reports the first suspicious bond. I think this does not affect my questions. Thank you very much. Best regards, Mario -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Changing constraints algorithm.

Dear all, A question arises to me when thinking about the more robustness of LINCS with respect to SHAKE: is it well known that LINCS preserves the symplecticness of the Verlet integrators? Thank you very much. Best regards, Mario 2014-10-08 22:31 GMT+02:00 Mark Abraham mark.j.abra

[gmx-users] Relation between bonds and nstlist

Dear all, Is it possible that the choice of the value of nstlist can have any influence in the behaviour of the bonds between atoms? Any further coment, suggestion or reference would be very much appreciated. Thank you very much. Best regards, Mario Fernández-Pendás -- Gromacs Users mailing

Re: [gmx-users] Implementation of SHAKE

Hi Mark, There was something in the matrix calculations that was not totally clear to me. That is why I started to think in a different approach. Now everything is fine. Thank you very much, Mario Fernández-Pendás El 23/10/2014 01:15, Mark Abraham mark.j.abra...@gmail.com escribió: Hi

[gmx-users] Implementation of SHAKE

://onlinelibrary.wiley.com/doi/10.1002/1096-987X%2820010415%2922:5%3C501::AID-JCC1021%3E3.0.CO;2-V/abstract Thank you very much. Cheers, Mario Fernández-Pendás -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] Velocity Verlet integrator

for positions? My intuitive idea would be to update first one half for velocities, then a full step for positions and, finally, using these new positions the second half for velocities. Maybe I am missunderstanding something. Thank you very much, Mario Fernández-Pendás 2014-03-23 14:33 GMT+01:00 Michael

Re: [gmx-users] Velocity Verlet integrator

...@vt.edu: On 10/15/14 7:30 AM, Mario Fernández Pendás wrote: Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I

Re: [gmx-users] Velocity Verlet integrator

) minimizing communication and output. It is not as elegant as it should be. There are efforts to clean this up, but it's a lot of reorganization, and has gone slowly. On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás mariof...@gmail.com wrote: Yes, I understand that. But my

Re: [gmx-users] Velocity Verlet integrator

control, there are many cases that you cannot really join the steps as well. On Wed, Oct 15, 2014 at 10:05 AM, Mario Fernández Pendás mariof...@gmail.com wrote: Thank you very much Professor Shirts. I have these doubts because I am trying to implement new integrators based