Re: [gmx-users] Removing periodic boundary conditions on a dimer

sually worked for me, but I used to run > simulations on old versions of Gromacs so it might be deprecated. > trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc mol > > > Il mar 23 apr 2019, 10:51 Nawel Mele ha scritto: > > > Dear Gromacs users, > > >

[gmx-users] Removing periodic boundary conditions on a dimer

be using with these kind of system, do you have any suggestions ? Many thanks, Regards -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Domain decomposition fatal error during production run

sed with what exactly happen here, when I looked at the COM distance between the two monomers it is fluctuating around 2.6 nm but does not go higher than 3 nm or less than 2.5 nm. Can anyone help me here? Many thanks, Regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840

[gmx-users] pull code, help pulling monomers in the same direction

ns due to the minus sign it pulls to opposite direction pull_k1 =1000 ; kJ mol^-1 nm^-2 Many thanks in advance, Regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- Gromacs Users mailing list * Please search the archive at h

[gmx-users] modified peptide parametrization

such as CGenFF or antechamber in the case of small molecule but for modified peptides? Or guide me on the path to follow for such parametrization. Many thanks, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- Gromacs Users mailing list * Please search the archive

[gmx-users] Umbrella sampling, choice of number of windows

would like to know if there is a protocol to determine how many windows to use ? Best regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Problem reading pdb files

1 32.320 27.010 11.290 1.00 0.00 ATOM 29 N3 MOL 1 0.260 26.420 10.890 1.00 0.00 TER ENDMDL Nawel -- Nawel Mele, PhD Research Student Jonathan W Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- Gromacs Users mailing

[gmx-users] Problem reading pdb files

1 32.320 27.010 11.290 1.00 0.00 ATOM 29 N3 MOL 1 0.260 26.420 10.890 1.00 0.00 TER ENDMDL -- Nawel Mele, PhD Research Student Jonathan W Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- Gromacs Users mailing list

Re: [gmx-users] Fwd: PCA two ensembles different atoms order

rtily invite the rest of the list to chip in. > > Could it be that there's simply poor correlation between your > simulations and your NMR ensemble? > > > Peter > > > On 03-07-17 12:34, Nawel Mele wrote: > > Hi Peter, > > > > What I have is two REMD

[gmx-users] Fwd: PCA two ensembles different atoms order

ct both ensembles on those PCs to get > comparable results. > > > Peter > > > On 03-07-17 11:37, Nawel Mele wrote: > > Hi all , > > > > When performing a PCA of two different ensembles of the same molecule the > > atoms of each molecule need to be in th

[gmx-users] PCA two ensembles different atoms order

I combined the ensemble they don't " like each other " like if they weren't the same molecule so don't have the same topology , I don't know if it clear . Does anyone had to deal with that ? Regards, Nawel -- Nawel Mele, PhD Research Student Jonathan W Essex Group, School of Chemistry Unive

[gmx-users] PCA two ensembles different atoms order

I combined the ensemble they don't " like each other " like if they weren't the same molecule so don't have the same topology , I don't know if it clear . Does anyone had to deal with that ? Regards, Nawel -- Nawel Mele, PhD Research Student Jonathan W Essex Group, School of Chemistry Unive

[gmx-users] Principale component analysis , experiment and MD comparison

separately and NMR separately and plot the result in one figure to see the difference between the two methods and now I am confused on the process to compare different MD with experimental data or even with a random generator. Any ideas? Regards -- Nawel Mele, PhD Research Student Jonathan W Essex

Re: [gmx-users] demux.pl input file

2015-09-02 21:38 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/2/15 9:21 AM, Nawel Mele wrote: > >> 2015-09-02 14:09 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 9/2/15 8:48 AM, Nawel Mele wrote: >&

Re: [gmx-users] demux.pl input file

to concatenate the log files of replica "0". > Regards, > > Andrea > > 2015-09-02 12:16 GMT+02:00 Nawel Mele <nawel.m...@gmail.com>: > > > Dear Users, > > > > I have performed a REMD simulation on a protein with 48 replicas. I have > > 400

[gmx-users] demux.pl input file

run2_1.log ... runx_1.log > run_total.log cat run1_0.log run1_1.log run1_2.log...run1_47.log run2_0.log run2_1.log run2_2.log... run2_47.log ... runx_0.log runx_1.log runx_2.log ...runx_47.log > run_total.log Many thanks for your help. Nawel --

Re: [gmx-users] demux.pl input file

edu>: > > > On 9/2/15 6:35 AM, Nawel Mele wrote: > >> Dear Andrea, >> >> Thank you very much for your quick answer. >> >> I would like to ask you another quick question. Like I said I am >> interested >> on a particular temperature , so I wante

Re: [gmx-users] demux.pl input file

2015-09-02 13:38 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/2/15 8:33 AM, Nawel Mele wrote: > >> Dear Justin, >> >> Thank you for your answer, >> >> So from the REMD simulation we get different output files: >> - .trr : trajectory f

Re: [gmx-users] demux.pl input file

2015-09-02 14:09 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/2/15 8:48 AM, Nawel Mele wrote: > >> 2015-09-02 13:38 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 9/2/15 8:33 AM, Nawel Mele wrote: >>> &g

[gmx-users] REMD temperature trajectory

that mean that, except for the first column, each column corresponds to each temperature? An so from that we can follow the trajectory of the replicas for a temperature of interest? Many thanks in advance Nawel -- Nawel Mele, PhD Research Student Jonathan Essex Group, School of Chemistry University

Re: [gmx-users] REMD mdrun_mpi error

On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele nawel.m...@gmail.com wrote: Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to equilibrate my system I get this error : Double sids (0, 1) for atom 26 Double

[gmx-users] REMD mdrun_mpi error

=00:10:00#PBS -o zzz.qsub.out#PBS -e zzz.qsub.errmodule load openmpi module load gromacs/4.6.5mpirun -np 48 mdrun_mpi -s eq_.tpr -multi 48 -replex 10 faillog-X.log* Does anyone have seen this issue before?? Many thanks, -- Nawel Mele, PhD Research Student Jonathan Essex Group, School