[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 2018.2 (single precision)Changing nstlist from 20 to 80, rlist from 1.224 to 1.32Using 1 MPI processUsing 16 OpenMP threads Back Off! I just backed up md.xtc to ./#md.xtc.2#Back Off! I just backed up md.trr to ./#md.trr.2#Back Off! I just backed up md.edr to ./#md.edr.2#starting mdrun 'Protein in water'3000 steps, 6.0 ps. I built gromacs with MPI=on and CUDA=on and the compilation process looked good. I ran gromacs 2018.2 with CUDA 5 months ago and it worked, but now it doesn't work. Information from *.log file: GROMACS version: 2018.2Precision: singleMemory model: 64 bitMPI library: MPIOpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU support: CUDASIMD instructions: AVX_512FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512RDTSCP usage: enabledTNG support: enabledHwloc support: disabledTracing support: disabledBuilt on: 2018-06-24 02:55:16Built by: vlad@vlad [CMAKE]Build OS/arch: Linux 4.13.0-45-generic x86_64Build CPU vendor: IntelBuild CPU brand: Intel(R) Core(TM) i7-7820X CPU @ 3.60GHzBuild CPU family: 6 Model: 85 Stepping: 4Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apicC compiler: /usr/bin/cc GNU 5.4.0C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 5.4.0C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda-9.2/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Wed_Apr_11_23:16:29_CDT_2018;Cuda compilation tools, release 9.2, V9.2.88CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;; ;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;CUDA driver: 9.10CUDA runtime: 32.64NOTE: Detection of GPUs failed. The API reported:GROMACS cannot run tasks on a GPU. Any idea what I am doing wrong? Best,Vlad -- C уважением, Владимир А. Богданов -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 Energy = -3.0612996e+04 Maximum force = 9.8396473e+00 on atom 3209 Norm of force = 1.0086957e+00 However, when I started NVT production, I see the potential of the system goes up to a positive value Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 7.61233e+048.43296e+022.83000e+042.89344e+026.94750e+04 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.58903e+04 -8.17942e+04 -1.07861e+045.24188e+035.14340e+03 PotentialKinetic En. Total Energy Conserved En.Temperature 7.69455e+041.16251e+051.93197e+05 -7.02956e+043.00338e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -3.58345e+022.99966e+026.24109e-05 I don't know what happened and why the potential goes up. Should I worry about this? Thanks ِAli -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 Sorbo Sent: Tuesday, January 29, 2019 1:15 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [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 tried with -ip file.dat but still I didn't get what I want. Do you have any suggestions? Thanks Best, Giuseppe -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 tried with -ip file.dat but still I didn't get what I want. Do you have any suggestions? Thanks Best, Giuseppe -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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-couple Perinnelo-Rahmen, Pcouple type = surface-tension or semiisotropic, compressibility = 4.5e-5 4.5e-5 , ref P =10 ref temp 300 or 400K and run for 0.5 ns What occurs is a few molecules from the cube form ( apparently ) a gas phase. What I expected was the water to expand to fill the enlarged box. My run time may be too short so I'll run longer times later. But are my expectations incorrect - should not all the water expand ?I used an mpd type NPT - should I use NVE and if so how does that differ from NPT other than setting tcoupl = no and pcoupl = no. I can - and will - try this but it may be an incorrect approach as well Paul -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 gpu -ntomp 5 -ntmpi 10 -npme 1 -gputasks 1 or mdrun -deffnm file -nb gpu -pme gpu -ntomp 5 -ntmpi 10 -npme 1 -gpu_id 01 this may help select both hope it helps Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of praveen kumar Sent: Tuesday, January 29, 2019 10:59 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [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 mdrun -v -deffnm test getting this message Using 1 MPI process Using 10 OpenMP threads 1 GPU auto-selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this nodes: It seems simulation runs by make use of one GPU instead of two. I have checked it using nvidia-smi. similar error has got already in the given link https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- users/2018-April/119915.html I have tried all those options given by Mark and other people, I am wondering whether this issue cab be solved ? I.e. Make use of two gpu cards for one simulation run I would be really thankful to if anyone can help me in this regard. Thanks Praveen -- Thanks & Regards Dr. Praveen Kumar Sappidi, National Post Doctoral Fellow. Computational Nanoscience Laboratory, Chemical Engineering Department, IIT Kanpur, India-208016 -- Thanks & Regards Praveen Kumar Sappidi, National Post Doctoral Fellow. Computational Nanoscience Laboratory, Chemical Engineering Department, IIT Kanpur, India-208016 -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 generated itp file.
If "-merge" is missing, only the intra-chain SS bonds are shown in the
individual itp files.
So happy to see the martini forum come back!
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 29, 2019 11:03 PM
To: "gromacs.org_gmx-users";
Subject: 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 only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
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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 medium
for these martini specific questions.
From: ZHANG Cheng
Sent: 29 January 2019 16:08
To: gromacs.org_gmx-users
Subject: [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 – HC220
) Intrachain disulfide of LC: LC23 – LC88, LC134 – LC194
) Intrachain disulfide of HC: HC144 – HC200, HC96 – HC22
Using this command will only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
--
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[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 only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
--
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
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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 martini itp files? Dear martini friends, By default, the "martinize.py" will 1) for backbone atoms, positively charge the N-terminus (atom type Qd), and negatively charge the C-terminus (atom type Qa). 2) for side chain chargeable residues, always positively charge the LYS and ARG and negatively charge the ASP and GLU. Now I want to change the protonation states based on a particular pH as determined by pdb2pqr server. 1) For backbones, if my N-terminus residue is MET: 1Qd 1 METBB 1 1. ; C 2C5 1 MET SC1 2 0. ; C based on "martini_v2.2P_aminoacids.itp" for MET: ;id type resnr residu atom cgnr charge 1 P5 1 MET BB 1 0 2 C5 1 MET SC12 0 should I change to this? 1P5 1 METBB 1 0. ; C 2C5 1 MET SC1 2 0. ; C 2) For side chains, e.g. GLU 362P5 165 GLUBB 362 0. ; C 363Qa 165 GLU SC1 363 -1. ; C if I do not want GLU to be negatively charged, based on "martini_v2.2P_aminoacids.itp" for GLU neutral form: ;id type resnr residu atom cgnr charge 1 P5 1 GLU0BB 1 0 2 P1 1 GLU0SC12 0 should I change to this? 362P5 165 GLU0 BB 362 0. ; C 363P1 165 GLU0 SC1 363 0. ; C Thank you! Yours sincerely Cheng -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 is no difference in size. So the Ix Iy Iz values should be comparable in both the aggregate and not 4x times different.I want to know why the the Ix Iy Iz values are 4x times different when the shape dimensions are similar. The aggregate size is similar. Thanks in advance Aishwarya -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 means that the size of the aggregates are comparable and there is no difference in size. So the Ix Iy Iz values should be comparable in both the aggregate and not 4x times different.I want to know why the the Ix Iy Iz values are 4x times different when the shape dimensions are similar. The aggregate size is similar. Thanks in advance Aishwarya On Tue, Jan 29, 2019 at 10:45 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: Radius of gyration and moment of inertia (Dallas Warren) >2. How to adjust the default protonation states in martini itp > files? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) >3. trap invalid opcode (Schulz, Roland) >4. About fprintf and debugging (Schulz, Roland) >5. Re: How to adjust the default protonation states in martini > itp files? (Peter Kroon) > > > -- > > Message: 1 > Date: Tue, 29 Jan 2019 09:11:55 +1100 > From: Dallas Warren > To: GROMACS users > Subject: Re: [gmx-users] Radius of gyration and moment of inertia > Message-ID: > 2yxumfbdwd27yjwczbmw8dptlnwp...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123938.html > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On Sat, 26 Jan 2019 at 05:11, Aishwarya Dhar > wrote: > > > Hi, > > I am trying to find the moment of inertia of an aggregate. > > I have used the command gmx gyrate -f test.gro -s test.gro -p yes -mol > > yes -o out.xvg > > > > For two aggregates the the shape is similar but the values are > > very different for Ix Iy Iz > > > > For an aggregate 1 > > Ix Iy Iz > > 81538.8 243689 251837 > > > > For aggregate 2 > > Ix Iy Iz > > 144172 498275 517148 > > Could you please help me as what could the possible solution? > > > > > > > > Thanks in advance > > -- > > 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 > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Message: 2 > Date: Tue, 29 Jan 2019 08:38:14 +0800 > From: "=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=" <272699...@qq.com> > To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?=" > > Subject: [gmx-users] How to adjust the default protonation states in > martini itp files? > Message-ID: > Content-Type: text/plain; charset="ISO-8859-1" > > Dear martini friends, > > > By default, the "martinize.py" will > > > 1) for backbone atoms, positively charge the N-terminus (atom type Qd), > and negatively charge the C-terminus (atom type Qa). > > > 2) for side chain chargeable residues, always positively charge the LYS > and ARG and negatively charge the ASP and GLU. > > > Now I want to change the protonation states based on a particular pH as > determined by pdb2pqr server. > > > 1) For backbones, if my N-terminus residue is MET: > 1Qd 1 METBB 1 1. ; C > 2C5 1 MET SC1 2 0. ; C > > > > based on "martini_v2.2P_aminoacids.itp" for MET: > ;id type resnr residu atom cgnr charge > 1 P5 1 MET BB 1 0 > 2 C5 1 MET SC12 0 > > > > should I change to this? > 1P5 1 METBB 1 0. ; C > 2C5 1 MET SC1 2 0. ; C > > > > 2) For side chains, e.g. GLU > 362P5 165 GLUBB 362 0. ; C > 363Qa 165
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 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 >> >> >> 1) for backbone atoms, positively charge the N-terminus (atom type Qd), and >> negatively charge the C-terminus (atom type Qa). >> >> >> 2) for side chain chargeable residues, always positively charge the LYS and >> ARG and negatively charge the ASP and GLU. >> >> >> Now I want to change the protonation states based on a particular pH as >> determined by pdb2pqr server. >> >> >> 1) For backbones, if my N-terminus residue is MET: >> 1Qd 1 METBB 1 1. ; C >> 2C5 1 MET SC1 2 0. ; C >> >> >> >> based on "martini_v2.2P_aminoacids.itp" for MET: >> ;id type resnr residu atom cgnr charge >> 1 P5 1 MET BB 1 0 >> 2 C5 1 MET SC12 0 >> >> >> >> should I change to this? >> 1P5 1 METBB 1 0. ; C >> 2C5 1 MET SC1 2 0. ; C >> >> >> >> 2) For side chains, e.g. GLU >> 362P5 165 GLUBB 362 0. ; C >> 363Qa 165 GLU SC1 363 -1. ; C >> >> >> >> if I do not want GLU to be negatively charged, >> >> >> based on "martini_v2.2P_aminoacids.itp" for GLU neutral form: >> ;id type resnr residu atom cgnr charge >> 1 P5 1 GLU0BB 1 0 >> 2 P1 1 GLU0SC12 0 >> >> >> >> should I change to this? >> 362P5 165 GLU0 BB 362 0. ; C >> 363P1 165 GLU0 SC1 363 0. ; C >> >> >> >> Thank you! >> >> >> Yours sincerely >> Cheng -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 > > > 1) for backbone atoms, positively charge the N-terminus (atom type Qd), and > negatively charge the C-terminus (atom type Qa). > > > 2) for side chain chargeable residues, always positively charge the LYS and > ARG and negatively charge the ASP and GLU. > > > Now I want to change the protonation states based on a particular pH as > determined by pdb2pqr server. > > > 1) For backbones, if my N-terminus residue is MET: > 1Qd 1 METBB 1 1. ; C > 2C5 1 MET SC1 2 0. ; C > > > > based on "martini_v2.2P_aminoacids.itp" for MET: > ;id type resnr residu atom cgnr charge > 1 P5 1 MET BB 1 0 > 2 C5 1 MET SC12 0 > > > > should I change to this? > 1P5 1 METBB 1 0. ; C > 2C5 1 MET SC1 2 0. ; C > > > > 2) For side chains, e.g. GLU > 362P5 165 GLUBB 362 0. ; C > 363Qa 165 GLU SC1 363 -1. ; C > > > > if I do not want GLU to be negatively charged, > > > based on "martini_v2.2P_aminoacids.itp" for GLU neutral form: > ;id type resnr residu atom cgnr charge > 1 P5 1 GLU0BB 1 0 > 2 P1 1 GLU0SC12 0 > > > > should I change to this? > 362P5 165 GLU0 BB 362 0. ; C > 363P1 165 GLU0 SC1 363 0. ; C > > > > Thank you! > > > Yours sincerely > Cheng -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
