Re: [gmx-users] How to adjust the default protonation states in martini itp files?

Hi Zhang, I'm fairly sure GLU0 does what you want, but I'm not 100% sure on the terminus. It'll probably do what you want, but I've forwarded your question to the group to be sure. Peter On 29-01-19 01:38, ZHANG Cheng wrote: > Dear martini friends, > > > By default, the "martinize.py" will >

Re: [gmx-users] How to adjust the default protonation states in martini itp files?

I got an answer :) > The GLU0 is good indeed. For the termini, it depends on the secondary structure. Coil is the most likely for a terminus, so P5 should be OK. Note that there is a -nt option in martinize that sets neutral termini. > Jonathan Peter On 29-01-19 10:44, Peter Kroon wrote: > Hi

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 177, Issue 90

Re: Radius of gyration and moment of inertia (Dallas Warren) Yes of course the ratios are similar. The shapes are similar But when I measure the distance of the two agrregates in VMD , the length of the aggregates and the width of the aggregates are more or less of the same dimensions. Which mean

Re: [gmx-users] Radius of gyration and moment of inertia (Dallas Warren)

Hi, Yes of course the ratios are similar. The shapes are similar But when I measure the distance of the two agrregates in VMD , the length of the aggregates and the width of the aggregates are more or less of the same dimensions. Which means that the size of the aggregates are comparable and there

Re: [gmx-users] How to adjust the default protonation states in martini itp files?

Dear Peter, Thank you very much! I will use GLU0 and -nt. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 29, 2019 08:38 AM To: "gromacs.org_gmx-users"; Subject: How to adjust the default protonation states in m

[gmx-users] How to set the inter-chain disulfind bond in martini?

Dear Martini friends, My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy chain (HC): ) Interchain disulfide bond: LC214 ?C HC220 ) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194 ) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22 Using this command will

Re: [gmx-users] How to set the inter-chain disulfind bond in martini?

Hi Cheng, What’s the distance between the two interchain SG atoms? You can either tune the distance used for autodetecting cys bonds, or just specify all of them using the command line. Try `python martinize.py -h` Peter PS. The cgmartini.nl forum is also back online, which might be a better me

Re: [gmx-users] How to set the inter-chain disulfind bond in martini?

Dear Peter, Thank you, I find the answer now. Sorry I was using a pdb that the SS length is too long to form the SS bond. After changing to a correct one, I got the solution. I think, if we have more than one chain, we MUST use "-merge" option, so that the interchain SS bond can shown in the

[gmx-users] multiple GPU usage for simulation

Dear gromacs users I am working on molecular simulation using gromacs 2018.4, we have a new gpu machine which has two GPU cards. I have new workstation with 20 cores (Intel I9 processors) with 3.3 GHz Nvidia Getforce X1080 Ti cards(2 nos) I have tried running simulation using the command gmx

Re: [gmx-users] multiple GPU usage for simulation

I am not expert on this subject but have recently gone through the exercise... Firstly, does nvidia-smi indicate both cards are active ? Secondly, for the nvt or npt runs have you tried mdrun commands similar to : mdrun -deffnm file -nb gpu -gpu_id 01 or mdrun -deffnm file -nb gpu -pme

[gmx-users] modeling evaporation NVP NVE

Dear Users, I am trying to understand a model of water evaporation and am asking for a few of suggestions or just point to a link. So far I have modeled 1 molecules of spce water and equilibrated to a density near 1 gm/cc. I then double the size of the box and then using p-coupl

[gmx-users] how can I get two parallel lysin in the same box?

Dear all, I am using gromacs 5.1.2 and I am doing simulation with lysin and surfactant. Now in the same box I want two lys30 (two identical lysin) oriented once in parallel and once in orthogonal each other. I tried using gmx insert-molecules ... but it's a random orientation. I also tri

Re: [gmx-users] how can I get two parallel lysin in the same box?

Giuseppe, Use Avogadro, import or construct the four ( if I understand your model ) molecules in the desired orientations. Save as a pdb. Used editconf to construct the box. Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Giuseppe R Del Sor

[gmx-users] High potential energy

Hello GMX users I'm simulating a complex system. I started with energy minimization step which went fine then followed by a short NPT for equilibration then followed by energy minimization for more minimization and its output as below Steepest Descents converged to Fmax < 10 in 3783 steps Potential

[gmx-users] Gromacs 2018.5 with CUDA

Hey everyone! I need help, please. When I try to run MD with GPU I get the next error: Command line:gmx_mpi mdrun -deffnm md -nb autoBack Off! I just backed up md.log to ./#md.log.4#NOTE: Detection of GPUs failed. The API reported:GROMACS cannot run tasks on a GPU.Reading file md.tpr, VERSION 2018.