Re: [gmx-users] 回覆︰ Simulations with SWM4-DP water model in non PBC

Den 2018-08-13 kl. 11:49, skrev Chi Yuen Pak: Dear Prof. van der Spoel, Thanks for your reply. I tried touse the following commands (2 OpenMP threads): gmx_mpi grompp -f eq.mdp -c em.gro-p swm4-dp.top -r posre.gro -o eq.tpr mpirun -np 1 gmx_mpi mdrun -ntomp 2-deffnm eq Did you try

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Thank you for your reply! Best regards, Mahsa On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham wrote: > Hi, > > You need a composite selection, eg of an atomtype and residue type or > molecule type. Make a selection of the atomtype and another of whatever > seems suitable, and combine them. > >

[gmx-users] Gromacs 2018 support Radeon GPU?

Hi! I want to using GROMACS on my PC(Mac OS). There is an error in the installation of “make" process. My computer has 3.2GHz Intel Xeon W processor and Radeon Pro Vega 56 8176MB GPU. (iMac pro default) 1) My computer is appropriate for GROMACS? 2) Can I use GPU for mdrun? If it’s possible, I

Re: [gmx-users] 回复:Re: 回复:Re: Mixing rule between organic and inorganic units

Hi, There's a fundamental difference between a a calculation and a simulation, which is that the latter can defend its claim to model reality. Anybody can put parameters into an equation. Mark On Mon, Aug 13, 2018, 18:49 Justin Lemkul wrote: > > > On 8/13/18 11:47 AM, Baolin Huang wrote: > >

Re: [gmx-users] Gromacs 2018 support Radeon GPU?

Hi, You can probably get GPU support via the OpenCL implementation in GROMACS. Check out the installation guide, and get the most recent version of everything. Mark On Mon, Aug 13, 2018, 20:18 김나연 wrote: > Hi! I want to using GROMACS on my PC(Mac OS). > There is an error in the installation

[gmx-users] trjconv (File input/output error)

Dear gromacs users For fixing PBC problem, I used following command: gmx_mpi trjconv -f md.trr -s md.tpr -n index.ndx -o new.xtc -pbc nojump But I encountered with: Program gmx trjconv, VERSION 5.1.3 Source code file: /root/gromacs_source/gromacs-5.1.3/src/gromacs/utility/futil.cpp, line: 469

Re: [gmx-users] No default Ryckaert-Bell. types

Hello, This is telling you that the OPLS-AA force field does not have the dihedral force-field parameters for your molecule (topol_Other_chain_C.itp) of the Ryckaert-Bell type. Your exact problem might be: (1) There is something wrong with the molecule topology. (2) OPLS-AA really doesn't have

Re: [gmx-users] trjconv (File input/output error)

Den 2018-08-13 kl. 20:56, skrev Andrew Bostick: Dear gromacs users For fixing PBC problem, I used following command: gmx_mpi trjconv -f md.trr -s md.tpr -n index.ndx -o new.xtc -pbc nojump But I encountered with: Program gmx trjconv, VERSION 5.1.3 Source code file:

[gmx-users] Umbrella Sampling: At diff force constant

Dear All: I am doing umbrella sampling for a dimer (Consist of two molecules stacking together, no physical bond). I tried different force constants, I got different PMF for each of them. Could you suggest me, How reliably can I choose force constant. Followings are the settings: ; Pull code

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Dear Mark, Could you please comment on my previous question? I would really appreciate it. Best regards, Mahsa On Sat, Aug 11, 2018 at 12:52 PM, Mahsa wrote: > Hi Mark, > > Thank you for your reply! > > I tried gmx make_ndx -f topol.tpr -o index.ndx before and then selected > based on the

Re: [gmx-users] force/time application for pull

Hello Mark, Thank for your clarification. Gromacs pulling has simple protocol for pulling using umbrella sampling. Where one can only get f/t and x/t . here t is linearly increases for both cases of force and distance. That actually not full fill the need of experimental pulling. On Mon, Aug

Re: [gmx-users] Mixing rule between organic and inorganic units

Hi, What experimental data can you replicate to show the model is valid? Mark On Mon, Aug 13, 2018, 17:34 Baolin Huang wrote: > Dear All, >I studied the interactions between BMP-2 (protein) and hydroxyapatite > (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The >

[gmx-users] 回覆︰ Simulations with SWM4-DP water model in non PBC

Dear Prof. van der Spoel, Thanks for your reply. I tried touse the following commands (2 OpenMP threads):   gmx_mpi grompp -f eq.mdp -c em.gro-p swm4-dp.top -r posre.gro -o eq.tpr mpirun -np 1 gmx_mpi mdrun -ntomp 2-deffnm eq   but this gave me the following errormessage in GROMACS 2018.2:

Re: [gmx-users] force/time application for pull

Dear Justin. Thanks for your kind advise. But why don't it is not possible to apply the constant force which should increases linearly (at each instant of time delta) like at t1 -f1 t2-f2 . . tn-fn and corresponding to that force we get extension for each increment of time in Gromacs. This is

Re: [gmx-users] force/time application for pull

Hi, It's possible, but there is no code written for it. Mark On Mon, Aug 13, 2018, 12:47 Rakesh Mishra wrote: > Dear Justin. > > Thanks for your kind advise. > But why don't it is not possible to apply the constant force which should > increases linearly (at each instant of time delta) >

Re: [gmx-users] force/time application for pull

On 8/13/18 6:38 AM, Rakesh Mishra wrote: Hello Mark, Thank for your clarification. Gromacs pulling has simple protocol for pulling using umbrella sampling. Where one can only get f/t and x/t . here t is linearly increases for both cases of force and distance. That actually not full fill the

Re: [gmx-users] force/time application for pull

Hi, Can you please share a link to something that indicates why this would be a good tool for modeling such experimental pulling scenarios? Making the case for implementing such a feature would benefit from that. Mark On Mon, Aug 13, 2018, 13:42 Rakesh Mishra wrote: > Hello Mark, > > Thank

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Hi, You need a composite selection, eg of an atomtype and residue type or molecule type. Make a selection of the atomtype and another of whatever seems suitable, and combine them. Mark On Sat, Aug 11, 2018, 13:53 Mahsa wrote: > Hi Mark, > > Thank you for your reply! > > I tried gmx make_ndx

[gmx-users] 回复:Re: Mixing rule between organic and inorganic units

Hi， I calculated the interaction energy（actually van der Waals part and electrostatic part），Rg，RMSD，and RMSF. regards， -- 该邮件从移动设备发送 --原始邮件-- 发件人："Mark Abraham "; 发送时间：2018年8月13日(星期一) 晚上11:02 收件人："gmx-users" ; 抄送："gromacs.org_gmx-users "; 主题：Re: [gmx-users]

[gmx-users] 回复:Re: 回复:Re: Mixing rule between organic and inorganic units

Hi all， That is a pure simulation work，no experimental data. The reviewer doubt the Lorentz-Berthelot combination rule for calculating the interaction energy between BMP-2 and HAP. I have to persuade the reviewer that the mixing rule works well in the BMP-2/HAP system. Thanks for your help.

Re: [gmx-users] 回复:Re: Mixing rule between organic and inorganic units

On 8/13/18 11:28 AM, Baolin Huang wrote: Hi， I calculated the interaction energy（actually van der Waals part and electrostatic part），Rg，RMSD，and RMSF. regards， I wouldn't think any of those are necessarily meaningful (interaction energy almost certainly isn't, and a decomposition between

Re: [gmx-users] 回复:Re: 回复:Re: Mixing rule between organic and inorganic units

On 8/13/18 11:47 AM, Baolin Huang wrote: Hi all， That is a pure simulation work，no experimental data. The reviewer doubt the Lorentz-Berthelot combination rule for calculating the interaction energy between BMP-2 and HAP. I have to persuade the reviewer that the mixing rule works well in

[gmx-users] Mixing rule between organic and inorganic units

Dear All, I studied the interactions between BMP-2 (protein) and hydroxyapatite (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The mixing rule was the Lorentz-Berthelot combination. A reviewer commented that 'The interaction of organic molecule on inorganic material needs