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

Hi all I want to calculate the order parameter of the NH vector for each amino acids of a protein in a gromacs trajectory for compare with NMR experimental data. I found that it can be calculated using rotacf to calculate the correlation time, when trying to run the program I get an error. In the

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.usp.b

[gmx-users] distance analysis error

Hi everbody I'm trying to analyse an preotein simulation made in Gromacs 2018, but when i send the command this returened to me this error: Inconsistency in user input: Selection 'F519' does not evaluate into an even number of positions (there are 1 positions) I made this index of both CB atoms

Re: [gmx-users] dssp error

; >> 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. > >>> I&

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

Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: g

[gmx-users] gpu cpu use

Hi everybody I have acces to one computer with 2 GPU and 2 CPU. Can i use both GPU and both CPU in a simulation? Each cCPU have 10 cores and 20 threads I'm trying whith this command: mpirun -np 4 gmx mdrun -ntomp 6 -gpu_id 00 but i don't undesrtand these numbers and i can use it Thanks for you

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

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

ar de 2019 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

[gmx-users] gromacs error in vacuum preparation simulation

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 gromacs send me this error: --- Program: gmx grompp, version 2018.6 Source file: src/gromacs/gmxpreproces

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

Good afternon. How can i calculate th S2 order parameters??? Thanks. Em qua, 19 de dez de 2018 às 11:51, Dr Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> escreveu: > Hi Everyone, > > Is the S2max and S2min produced by gmx chi is same as Ss (slow order > parameter)and Sf (fast order p

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

pi cbd211_md.cpt -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 fo

[gmx-users] Recovery simulation error

Hi Gromacs Users. I has been a simulation with gromacs 2016 but my simulation stopped by an energy break. i try to restar in the last checkpoint but this does work and send me this error: Expected output files not present or named differently: cbd211_md.log cbd211_md.xtc cbd211_md.trr cbd21

[gmx-users] GPU ERROR RUNING A SIMULATION

Hi again every body. I'm tryin running a simulation of a protein in water using Gromacs 2018.3. When i try to minimize the energy in NVT equilibration this send me this error during mdrun: Reading file cbd12_nvt.tpr, VERSION 2018.3 (single precision) Multiple energy groups is not implemented for G

Re: [gmx-users] simulation error

às 08:36, 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]: > >

Re: [gmx-users] simulation error

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

Hi everyone. I'm trying simulate a protein in water followin lysozyme tutorial using gromacs 2016.3. When triying minimize the system after make the box and insert a salt concentration the minimization has been stoped sendingme the following error: step 16: One or more water molecules can not be s