Re: [gmx-users] Graphene sheet topology

Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I created a graphene.top file according to the

[gmx-users] Graphene sheet topology

Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I created a graphene.top file according to the

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Great! I had already setup my git copy. No need for it. Strange atom names as usual. So we can already start our metalloenzyme simulation. Great software and support. Thank you Mark and Justin! 2016-04-22 21:49 GMT-03:00 Justin Lemkul : > > > On 4/22/16 8:40 PM, Pedro Lacerda

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

On 4/22/16 8:40 PM, Pedro Lacerda wrote: Applying the same simple conversion to the vdw parameters for atoms Mg+2 (id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER package, which is the base of Sorin parameters, there is agreement between Mg+2 and Zn+2. It looks like

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Applying the same simple conversion to the vdw parameters for atoms Mg+2 (id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER package, which is the base of Sorin parameters, there is agreement between Mg+2 and Zn+2. It looks like a bug in the L-J parameters of TINKER package

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

For me they must be the same in both force fields amber99sb-ildn, amber99, at the paper, etc. If it is different then should be another force field, isn't it? About the conversion, I did it wrong on my spreadsheet. Sorry... It works! Many thanks! Except for the epsilon of Ca+2. I verified the

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

On 4/22/16 6:24 PM, Pedro Lacerda wrote: Thank you! According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+ used at AMBER package. Or the paper or GROMACS copied wrongly from the AMBER package source because simple unit conversion gives different results. That paper was

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Thank you! According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+ used at AMBER package. Or the paper or GROMACS copied wrongly from the AMBER package source because simple unit conversion gives different results. I don't own a copy of AMBER package, please could you verify the

Re: [gmx-users] Translational Pulling

Hi, Justin, Thank you so much. -- 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] Translational Pulling

On 4/22/16 5:34 PM, Ray Chao wrote: ​Hi, Justin, What I wanted to do in my.mdp file is to compress the third group C by moving group X and Z towards each other. So, it seems that I have to freeze X and Z first then pull the C towards X​. After relocating Z, then pull C towards Z. Why not

Re: [gmx-users] Translational Pulling

​Hi, Justin, What I wanted to do in my.mdp file is to compress the third group C by moving group X and Z towards each other. So, it seems that I have to freeze X and Z first then pull the C towards X​. After relocating Z, then pull C towards Z. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Translational Pulling

On 4/22/16 5:29 PM, Ray Chao wrote: ​Hi, Justin, I also notice that in Lammps, you seem to be able to set up the force and velocity to frozen groups.​ Does Gromacs have similar features? No. Frozen groups are frozen - they don't move, they don't have velocities, etc. Maybe LAMMPS is

Re: [gmx-users] Translational Pulling

​Hi, Justin, I also notice that in Lammps, you seem to be able to set up the force and velocity to frozen groups.​ Does Gromacs have similar features? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Translational Pulling

On 4/22/16 5:27 PM, Ray Chao wrote: ​Hi, Justin, Thanks for your response. I also tried to pull with absolute reference group. But it didn't work either. I saw in the manual that freezing means the position will no longer be updated. So technically, you cannot pull frozen atoms, right?​

Re: [gmx-users] Translational Pulling

​Hi, Justin, Thanks for your response. I also tried to pull with absolute reference group. But it didn't work either. I saw in the manual that freezing means the position will no longer be updated. So technically, you cannot pull frozen atoms, right?​ -- Gromacs Users mailing list * Please

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

OK, perfect, once the GPU is available (I'll kick the student ...) I 'll post reports of the results, to have a better description of what happens. Thanks for the short code, it will help! Cheers, Stéphane Le 22/04/2016 21:58, Szilárd Páll a écrit : Actually, here's a small program I hacked

Re: [gmx-users] Translational Pulling

On 4/22/16 3:51 PM, Ray Chao wrote: H ​i, Justin, Actually I was using freeze groups together with pulling. However, the atoms seemed to be frozen and weren't pulled away at all. Following is my mdp file: freezegrps = X Z freezedim= Y Y Y Y Y Y pull

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Actually, here's a small program I hacked up that will help diagnose such issues; you'll find the instructions and explanation of the expected output in the header of the file: https://github.com/pszi1ard/playground/blob/master/check-cuda-drv-runtime.cu Cheers, -- Szilárd On Fri, Apr 22, 2016

Re: [gmx-users] Translational Pulling

H​i, Justin, Actually I was using freeze groups together with pulling. However, the atoms seemed to be frozen and weren't pulled away at all. Following is my mdp file ​(Gromacs 5.0.7)​ : freezegrps = X Z freezedim= Y Y Y Y Y Y pull =

Re: [gmx-users] Translational Pulling

H ​i, Justin, Actually I was using freeze groups together with pulling. However, the atoms seemed to be frozen and weren't pulled away at all. Following is my mdp file: freezegrps = X Z freezedim= Y Y Y Y Y Y pull = umbrella

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Stéphane, Don't get me wrong, I don't think anyone was angry at your post - I certainly was not. On the contrary, describing this (rather annoying) problem and suggesting a solution is of good use for the GROMACS community -- and CUDA application user community in general. However, it is

Re: [gmx-users] Translational Pulling

On 4/22/16 12:44 PM, Ray Chao wrote: H ​i, gmx users, I want to simulate a system consisting two groups of atoms. One group of atoms are pulled towards the other group to compress it. But I also want to keep the atoms in pulling group "frozen". To be more specific, I want the center of mass

Re: [gmx-users] lennard jones

On 4/22/16 2:56 PM, Alexander Alexander wrote: Hello Mark, Here is the mssage: gmx grompp -f mini.mdp -c ni.gro -p topol.top -o mini.tpr Ignoring obsolete mdp entry 'optimize_fft' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# ERROR 1 [file mini.mdp]: With Verlet lists only

Re: [gmx-users] lennard jones

Hi, What was the actual error message, please? Mark On Fri, 22 Apr 2016 19:51 Alexander Alexander wrote: > Dear GMXuserr, > > To use LJ (6-9) in my simulation, I followed the manual as below: > > In .top file: > nbfunccomb-rule > 1 1 > >

[gmx-users] lennard jones

Dear GMXuserr, To use LJ (6-9) in my simulation, I followed the manual as below: In .top file: nbfunccomb-rule 1 1 In .mdp file: coulombtype = user vdWtype = user Also, I provided a table.xvg for LJ(6-9) in my working directory. Normally invoked the "gmx

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Le 22/04/2016 14:33, Szilárd Páll a écrit : Additionally, I suggest amending the post to note that the GDK and NVML that's picked up from it is optional and it is only useful with Quadro/Tesla cards. Dear Szilárd, I hope I'll find time to produce a proper bug report, but using the Ubuntu

[gmx-users] Translational Pulling

H ​i, gmx users, I want to simulate a system consisting two groups of atoms. One group of atoms are pulled towards the other group to compress it. But I also want to keep the atoms in pulling group "frozen". To be more specific, I want the center of mass of one group translate. while the atoms

[gmx-users] pdb2gmx parametrization of proteins consisted of metallo-bindings cofactor sites

Dear Gromacs users! I am interesting what full atomistic force field integrated in the current GMX is better to use for the pdb2gmx parametrization of the HEME containing proteins like cytochrome C (where cofactor is not covalently bound to the polypeptide chain). e.g -ff amber 99sb did not

[gmx-users] LJ (6-9)

Dear GMXuserr, To use LJ (6-9) in my simulation, I followed the manual as below: In .top file: nbfunccomb-rule 1 1 In .mdp file: coulombtype = user vdWtype = user Also, I provided a table.xvg for LJ(6-9) in my working directory. Normally invoked the "gmx

Re: [gmx-users] Long distance effects of mutation and stability

Hi, I hope this paper could help you. The title is "Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV‑1 Protease" dx.doi.org/10.1021/ja504096m| J. Am. Chem. Soc.2014, 136, 11956−11963 在 2016-04-21 04:34:26，"Jorge

Re: [gmx-users] Parallel GPU calculation on K80

-gpu_id provides the *per node* GPU to PP rank mapping, so you don't specify all GPUs, but list them per node in the order you want to assign them to your MPI ranks. -- Szilárd On Fri, Apr 22, 2016 at 10:17 AM, Yan Wang wrote: > Dear Gromacs Users, > Recently I have

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

On Thu, Apr 21, 2016 at 11:39 PM, Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 21/04/2016 03:54, treinz a écrit : > >> Hi, >> >> >> Can you also explain why the function calls to cudaDriverGetVersion() and >> cudaRuntimeGetVersion() both return 0, as in >> >>> >>CUDA

Re: [gmx-users] Defining LA atoms in .gro file

On Fri, Apr 22, 2016 at 9:25 PM, Groenhof, Gerrit wrote: > Hi again, > > From the error message it seems that the virtual_sites are not in the same > topology file. Since introduction of molecular topologies in GMX4, all QM > atoms must be in the same topology entry. It appears

Re: [gmx-users] Defining LA atoms in .gro file

Hi again, >From the error message it seems that the virtual_sites are not in the same >topology file. Since introduction of molecular topologies in GMX4, all QM >atoms must be in the same topology entry. It appears that in your case there >is a stretch of atoms, perhaps waters, in between the

[gmx-users] Calculating change in folding free energy due to mutation

Hi Everyone, I have a mutant (with 3 point mutation) whose Tm (melting temperature) is 6 degree C more than that of wild type protein. I think it will also have more negative folding free energy. Can anyone kindly guide me to calculate change in folding free energy between wild type protein and

Re: [gmx-users] Sometimes *.tpr.gro files aren't generated

Hi, It's always written if mdrun is permitted to shut down normally. But if the process is killed, eg by a job scheduler, then it can't do anything. Mark On Fri, 22 Apr 2016 11:23 yamashita.ryoto@st.kyoto-u.ac.jp < yamashita.ryoto@st.kyoto-u.ac.jp> wrote: > > Dear Gromacs users, > > >

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Le 22/04/2016 01:50, treinz a écrit : cudaGetDeviceCount returned 35 -> CUDA driver version is insufficient for CUDA runtime version Result = FAIL Unfortunately for any machine installed by now the setup is now as described, and works. There is one machine were this setup was not updated

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi Aswathy You can make a group with Protein and ligand in an index file using make_ndx and pass it with -n in gmx rms. Ashutosh On Fri, Apr 22, 2016 at 6:46 PM, Aswathy soman wrote: > Hi, > I have done a 100 ns simulation of protein-ligand complex. I was wondering

Re: [gmx-users] RMSD calculation of protein-ligand complex

You can make an index group with both protein+ligand using make_ndx command and use the index file from make_ndx to run the rmsd analysis Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi, You can create a group with the protein and the ligand using the make_ndx tool. Then you can use the created index file as input for your rmsd calculation. Cheers, On 22 Apr 2016 10:47, "Aswathy soman" wrote: > Hi, > I have done a 100 ns simulation of

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi, You must create a new índex group using make_ndx. Regards Pedro Lacerda Em 22/04/2016 06:47, "Aswathy soman" escreveu: > Hi, > I have done a 100 ns simulation of protein-ligand complex. I was wondering > is it possible to calculate RMSD of the entire

[gmx-users] RMSD calculation of protein-ligand complex

Hi, I have done a 100 ns simulation of protein-ligand complex. I was wondering is it possible to calculate RMSD of the entire protein-ligand complex. How to select the complex as such during the calculation of RMSD because there is no group as protein+ligand. Thanking you in advance Regards,

[gmx-users] Sometimes *.tpr.gro files aren't generated

Dear Gromacs users, I use Gromacs VERSION 5.0.6. Sometimes *.tpr.gro, *tpr.cpt, and *.tpr_prev.cpt files aren't generated (and *.tpr,*tpr.edr,*.tpr.log,*.tpr.trr are generated) when I do mdrun. I appreciate if you tell me the condition that *.tpr.gro files aren't generated. Thanks in

Re: [gmx-users] Catenation and Visualization

Hello Tsjerk Thank you for your response. I have applied periodic boundary conditions and have loaded only one file i.e. movie.pdb in Pymol. Thats correct I can turn visualization off but my question is why two objects are showing up when I have catenated two trajectories. That's I asked if used

[gmx-users] Parallel GPU calculation on K80

Dear Gromacs Users, Recently I have several calculation jobs which run on the K80 using GPU acceleration. There was six K80 cards in my cluster. As you all know, each K80 card has two cores. There were 12 number of the GPU in my cluster. When I used the option -gpu_id 01234567891011, the software

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119

On Thu, Apr 21, 2016 at 7:12 PM, Groenhof, Gerrit wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (ggro...@gwdg.de) Add cleanup rule >