[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs

Dear Users, I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for a RNA that has phosphate (P, OP1, OP2, OP3) on 5' . As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5' of RNA, pdb2gmx is giving an error. And so I want to add a 5'terminal PHOSPHATE

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Still did not work. change xMIC to xCore and log is below (if it was other way around, then originally it must have not worked). Script file is all oneline. -- Performing Test C_xCORE_AVX512_FLAG_WORKS -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed -- Performing Test

[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs

Dear Users, I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for a RNA that has phosphate (P, OP1, OP2, OP3) on 5' . As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5' of RNA, pdb2gmx is giving an error. And so I want to add a 5'terminal PHOSPHATE

Re: [gmx-users] gmx spatial

I would look at what you are using for the reference atoms around which the SDF is generated. Ideally they should be relatively rigid in position relative to each other, otherwise the SDF doesn't make as much sense. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Hi, On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn wrote: > Sorry for long wait on response, basically i followed the instruction at > nvidia website: > > http://www.nvidia.com/object/gromacs-installation.html > > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake.

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Sorry for long wait on response, basically i followed the instruction at nvidia website: http://www.nvidia.com/object/gromacs-installation.html I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After that it tells to run following: CC=gcc CXX=g++ cmake -DGMX_OPENMP=ON

Re: [gmx-users] error in nvidia cuda installation

Dear Mark and Stephane, Thanks a lot for your very usefull advices. Neda - Original Message - From: Stéphane Téletchéa To: gromacs org gmx-users Sent: Mon, 03 Jul 2017 22:20:31 +0430 (IRDT) Subject: Re:

Re: [gmx-users] error in nvidia cuda installation

Le 03/07/2017 à 17:48, Neda Rafiee a écrit : I am going to install GROMACS 5.1.4 which is enabled for parallelization, so I tried to install Cuda Nvidia as it is suggested in the gromacs website. I am using Linux Mint 18.1 Dear Neda, GROMACS + CUDA wroks best if you install the driver and

Re: [gmx-users] error in nvidia cuda installation

On Mon, Jul 3, 2017 at 5:59 PM Neda Rafiee wrote: > Dear users, > I am going to install GROMACS 5.1.4 which is enabled for parallelization, > so I tried to install Cuda Nvidia as it is suggested in the gromacs > website. I am using Linux Mint 18.1 > I tried to download Cuda

Re: [gmx-users] (Not-) Changing protonation when using pdb2gmx

Hi, You can use gmx pdb2gmx -lys interactively, or in a script with http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts, but you somehow have to know the order of the choices you want to make. On Mon, Jul 3, 2017 at 6:50 PM Hermann, Johannes < j.herm...@lrz.tu-muenchen.de>

[gmx-users] (Not-) Changing protonation when using pdb2gmx

Dear All, I am using pdb2gmx with the -lys flag in order to not protonate specific lysines. I have to do this for quit a few cases, where in most cases the lysines are protonated (as default in pdb2gmx). Is there a way to specify only the few cases, where I actually do not want to protonate

[gmx-users] error in nvidia cuda installation

Dear users, I am going to install GROMACS 5.1.4 which is enabled for parallelization, so I tried to install Cuda Nvidia as it is suggested in the gromacs website. I am using Linux Mint 18.1 I tried to download Cuda toolkit from its website but the link seems not to work properly at the present

[gmx-users] Problem reading pdb files

Hi all, I have two pdb files extracted from two trajectories of same compound but starting from two different configurations. I wanted to combined the two trajectories but I faced a broken structures behaviour while combining the two ensembles. I just attached two first frames of each

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

HI Peter, The correlation between the NMR and the simulation is pretty similar. I have analysed torsion angles distributions and they do sample similar area. When I performed the PCA I projected the NMR and REMD ensembles onto the NMR PCs. I have four different compounds and for each of them I

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

Hi Nawel, I'll admit that I'm out of my depth PCA-wise from here on out, so I heartily 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

Re: [gmx-users] Issue with the PDB generated after topology

Hi, Sure, they're all just labels. If you wanted to look at the heights of the girls in a family and the heights of boys in the same family, sorted by age, then e.g. boy 2 could easily be child 5... You just need to think about simulation residue number differently from input residue number.

[gmx-users] Issue with the PDB generated after topology

Thank you, Mark. I understand from your suggestion, that what I got from topology and solvation phases is correct, and MD simulations even if it affects the numbering of the structure but the simulation results remain unaffected and I could renumber my residues at the end of simulation as it

Re: [gmx-users] Issue with the PDB generated after topology

Hi, On Mon, Jul 3, 2017 at 11:34 AM Khadija Amine wrote: > Hi Mark, > > Is there any way to renumber my protein sequence at the end of the > simulation? > Sure gmx editconf -resnr, as Joao suggested is good. But you aren't going to get a sensible plot if residues in

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

Hi Peter, What I have is two REMD trajectories and an NMR ensemble. The two MD trajectories were not written in the same way in term of atoms order. So I just rewrite one of them to have the atoms in the pdb files in same order in term of indices and same for the NMR ensemble so all three

[gmx-users] (no subject)

1 F -- 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/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi Mark, *So, for the record, the actual issue is that GROMACS does not implement *some kind of tapering of non-bonded interactions that would apply between *particle pairs at short range? This is the extract from the supporting information of the paper I refer to that explains the issue

Re: [gmx-users] Issue with the PDB generated after topology

To renumber a gro file: gmx editconf -resnr OR Script it, I'm sure there's a one liner for that in awk (even in Python that shouldn't take more than 10 lines of code). /J On Mon, Jul 3, 2017 at 11:37 AM, Khadija Amine wrote: > Hi, > > I have already converted the .gro

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

Hi Nawel, I'm not quite sure what you're trying to achieve, or how, or what exactly is "wrong". In general though: calculate the principle components only once, for one of the ensembles, and project both ensembles on those PCs to get comparable results. Peter On 03-07-17 11:37, Nawel Mele

[gmx-users] Issue with the PDB generated after topology

Hi, I have already converted the .gro file to .pdb file and I'm not able to see the two separated chains. Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PCA two ensembles different atoms order

Hi all , When performing a PCA of two different ensembles of the same molecule the atoms of each molecule need to be in the same order ( same atom name associated to the same index) right ? However, my two ensembles, even being the same molecule ( different starting confirmation ), had their

[gmx-users] Issue with the PDB generated after topology

Hi Mark, Is there any way to renumber my protein sequence at the end of the simulation? The numbering is very important in RMSF plot for example. Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- Gromacs Users mailing list * Please search the

[gmx-users] protein protein interaction: side chain contribution

Hi all, I want to know the contribution of various amino acid side chain in complex that composed of 2 proteins. I used GROMOS53a6 forcefiel for the simulation. All parameters are as recommended by the concerned paper. I made separate index groups for each amino acid side chain and the proteins. I

Re: [gmx-users] Multiple output log. xtc .edr files generated using mpirun

Thanks Mark for your reply. In that case, it is confirmed that the problem is with the installation. I will try to get the package reinstalled. Thanks again. Best Regards, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Multiple output log. xtc .edr files generated using mpirun

Thanks Nikhil, for your response. But could I get a little more clue as to what mistake you are alluding to? I have again checked the link but I don't seem to find the mistake with the command. Thanks and Regards. Abhishek Acharya Research Associate, Department of Molecular Nutrition

Re: [gmx-users] Issue with the PDB generated after topology

Hi, I don't understand what you mean by "absent in terms of sequence." The chain is there, and must have a sequence of residues. It might not be numbered the same any more, since it is now part of a simulation, and not a set of chains. Mark On Sun, 2 Jul 2017 22:32 Khadija Amine

Re: [gmx-users] Grid Spacing

Hi, One issue here is that the parametrisation was not done with PME, so you need to look at how people have used it since, and how good their results were for systems similar to yours. Many GROMOS forcefield users prefer reaction field, which can be good enough for small solutes in homogeneous

Re: [gmx-users] Multiple output log. xtc .edr files generated using mpirun

Hi, You need MPI support to use more than one node at once. http://manual.gromacs.org/documentation/2016.3/install-guide/index.html#typical-installation Mark On Mon, 3 Jul 2017 07:29 Abhishek Acharya wrote: > Hello GROMACS users, > > I am trying to run a simulation

Re: [gmx-users] Multiple output log. xtc .edr files generated using mpirun

Hi, The problem is with your command see http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html -- 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

Re: [gmx-users] Grid Spacing

Hi, I think you need to refer the original papers for the ff. -- 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/Mailing_Lists * For (un)subscribe requests