Re: [gmx-users] Gromacs error

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-covar.html Has the following note (as does 'gmx help covar'): "Note that the diagonalization of a matrix requires memory and time that will increase at least as fast as than the square of the number of atoms involved. It is easy to run

[gmx-users] Gromacs error

Dear GROMACS Developers and users, While trying to clustering analysis based on certain distance matrices, however, while trying to perform PCA, I executed the following command, it shows the following error. Need your valuable suggestion and feedback to get rid of such errors. Thanking you

[gmx-users] Gromacs error while running energy minimization step

I got the following error while running the gromacs *NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected for

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 bad habit to > casually

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

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 bad habit to casually use -maxwarn as it overrides critical problems with your input. I see also this: WARNING 1

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

If i don't use -maxwarn option they send me the same error. I see also this: WARNING 1 [file topol.top, line 23986]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform

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

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 gromacs send me this error: --- Program:

[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:

Re: [gmx-users] Gromacs error

You really need cuda? IF no you can try:cmake .. -DGMX_GPU=OFF On Sunday, October 29, 2017, 7:26:04 AM GMT+2, Kunal Dutta wrote: Hi, I have the following problems kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..

[gmx-users] Gromacs error

Hi, I have the following problems kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message): The GROMACS build will download FFTW 3.3.3 as requested, but it will not know the file it

Re: [gmx-users] gromacs error

On 10/16/17 12:17 PM, Rahma Dahmani wrote: Hi, How can i rectify the following GROMACS error? Fatal error: atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms while sorting atoms. Either correct the atom names to what the force field expects, or simplify life and use

[gmx-users] gromacs error

Hi, How can i rectify the following GROMACS error? Fatal error: atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms while sorting atoms. Thank you for your help -- *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des Matériaux à l'état condensé,

Re: [gmx-users] gromacs error

Hi, It's hard to say, but you should look at the log file and terminal output, and install the latest in the series of bug fixes... 5.0.7 rather than choose a version known to have dozens more bugs... Mark On Tue, Sep 12, 2017 at 3:55 PM Vidya R wrote: > Hi, > > I

Re: [gmx-users] gromacs error

Hi, I fixed that error. However,I now encounter a new one... GROMACS:gmx grompp, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit Groenhof

Re: [gmx-users] gromacs error

Hi, Yeah I've never seen that, so I assume it's something weird related to how GROMACS was originally compiled vs how the system has been updated since. Since a rebuild is the way to investigate that, definitely update to at least the latest 5.0.x while you do it. Mark On Mon, Sep 11, 2017 at

Re: [gmx-users] gromacs error

On Mon, Sep 11, 2017 at 8:44 AM, Vidya R wrote: > Hi, > > > When I give these two commands > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > gmx mdrun -deffnm min > > I get this error. > > What to do? > > > > Reading file min.tpr, VERSION 5.0.2 (single precision) >

[gmx-users] gromacs error

Hi, When I give these two commands gmx grompp -f mdp/min.mdp -o min -pp min -po min gmx mdrun -deffnm min I get this error. What to do? Reading file min.tpr, VERSION 5.0.2 (single precision) tMPI error: tMPI Initialization error (in valid comm) Thanks, Vidya.R -- Gromacs Users mailing

Re: [gmx-users] Gromacs error: equilibration phase

Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you think anything is wrong. a) uploaded the coordinates of ligand "RND" on ATB server. I chose "heteromoelcule" molecule type. b) Entered the "net charge" by

Re: [gmx-users] gromacs error

On 8/29/17 12:09 AM, Neha Gupta wrote: Hi Vytautas, Thank you for your response.. I did as you told and got this message at the command prompt libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a But the error tells me : gmx: error while loading shared libraries:

Re: [gmx-users] gromacs error

Hi Vytautas, Thank you for your response.. I did as you told and got this message at the command prompt libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a But the error tells me : gmx: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such

Re: [gmx-users] gromacs error

Make sure you have libfftw3f installed properly. In such case command:whereis libfftw3fshould give you location of that file which gmx is unable to find. On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta wrote: Hi gromacs users, How to fix this error? gmx:

[gmx-users] gromacs error

Hi gromacs users, How to fix this error? gmx: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory PATH=$PATH:"/usr/local/gromacs/bin/" LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top" Thanks, Neha -- Gromacs

Re: [gmx-users] gromacs error

On 2/1/16 1:06 AM, Mehreen Jan wrote: how to run gromacs for protein protein interaction having phosphorylated at SER and THR. error: residue TPO not found in residue topology database modification are done from the given web. http://www.gromacs.org/Downloads/User_contributions/Force_fields

Re: [gmx-users] gromacs error

how to run gromacs for protein protein interaction having phosphorylated at SER and THR. error: residue TPO not found in residue topology database modification are done from the given web. http://www.gromacs.org/Downloads/User_contributions/Force_fields >make changes in .rtp file make changes in

[gmx-users] gromacs error

Hello I am doing Protein-Ligand simulation and I face following error while running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr". Kindly assist me how can I rectify error ? Error Program grompp, version 3.3.3 source code file: toppush.c, line: 1396

Re: [gmx-users] gromacs error

2015 7:33 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] gromacs error Hello I am doing Protein-Ligand simulation and I face following error while running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr". Kindly assist me how can I rectify error

Re: [gmx-users] Gromacs Error

Hi Manoj, The error is clear. Check the settings referred to in your .mdp file and modify them accordingly. Cheers, Tsjerk On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in wrote: Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation

Re: [gmx-users] Gromacs Error

ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist On Tue, May 19, 2015 at 10:25 AM, manoj damale manojaurangabad...@yahoo.co.in wrote: what exactly i should modify With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West

[gmx-users] Gromacs Error

Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation in nvt.mdp file mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr :-)  G  R  O  M  A  C  S  (-:    

[gmx-users] Gromacs error regarding default gromos bond type and angle type

Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the

[gmx-users] gromacs error

hi guys i have a problems with gromacs command .how can i can solve this problems: i install gromacs and i dont know what can i do: gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top No command 'gmx' found, did you mean: Command 'gcx' from package 'gcx' (universe)

Re: [gmx-users] gromacs error

On 9/22/14 10:14 AM, Yaser Hosseini wrote: hi guys i have a problems with gromacs command .how can i can solve this problems: i install gromacs and i dont know what can i do: gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top No command 'gmx' found, did you mean:

Re: [gmx-users] gromacs error

How should I correct the input file? Urszula Uciechowska On 7/31/14, 7:42 AM, Urszula Uciechowska wrote: Dear Gromacs users, I tried to run coarse grained MD however after a few steps I got: Step 39, time 0.78 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.038933,

Re: [gmx-users] gromacs error

On 7/31/14, 8:16 AM, Urszula Uciechowska wrote: How should I correct the input file? http://manual.gromacs.org/online/mdp_opt.html#vel And get your hands on some suitable tutorial material; proper use of these settings is routine. -Justin Urszula Uciechowska On 7/31/14, 7:42 AM,

Re: [gmx-users] gromacs error

Can anyone help me with this error file? I did not get the log file... Back Off! I just backed up md.log to ./#md.log.5# Reading file md10ns-2.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file md10ns.cpt generated: Mon Jul 21 20:45:14 2014 Gromacs binary or parallel settings not

Re: [gmx-users] gromacs error

On 7/31/14, 8:36 AM, Urszula Uciechowska wrote: Can anyone help me with this error file? I did not get the log file... There is no error here. I assume this is what is concerning: Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not