[gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 14
Kalyanashis Jana
kalyan.chem.in at gmail.com
Tue May 7 15:29:13 CEST 2019
On Tue, May 7, 2019 at 12:00 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Fwd: atoms are not part of any of the T-Coupling groups
> (ISHRAT JAHAN)
> 2. water mediated Hbond (spss4 at iacs.res.in)
> 3. Re: GROMOS 54A8 Force field (Mark Abraham)
> 4. Re: GROMOS 54A8 Force field (Mark Abraham)
> 5. Re: Error when compiling 2019.2 with -DGMX_MPI=ON (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 7 May 2019 11:11:37 +0530
> From: ISHRAT JAHAN <jishrat17 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Fwd: atoms are not part of any of the T-Coupling
> groups
> Message-ID:
> <CA+NjHRmPh8vGTZWRBPMmyKRGyx=
> GY-oDGkvDRf3ckJGUjfeiwQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> ---------- Forwarded message ---------
> From: ISHRAT JAHAN <jishrat17 at gmail.com>
> Date: Tue, May 7, 2019 at 11:05 AM
> Subject: atoms are not part of any of the T-Coupling groups
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
>
>
> Dear all,
> I am trying to calculate the lennard Jones interaction energy between
> protein and urea in the first solvation shell. I have made the index group
> of urea molecule in the first solvation shell and then tried to generate
> the .tpr file using that index. After running the command
> gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
> prot_u3M_rerun -n water_urea_5ofprot.ndx
> following error occur-
> 35099 atoms are not part of any of the T-Coupling groups
> part of .mdp file and index file is given below
> rvdw = 1.2^M
> fourierspacing = 0.12^M
> fourier_nx = 0^M
> fourier_ny = 0^M
> fourier_nz = 0^M
> pme_order = 4^M
> ewald_rtol = 1e-5^M
> optimize_fft = yes^M
> ; Berendsen temperature coupling is on in two groups^M
> Tcoupl = V-rescale^M
> tc-grps = Protein Urea_5ofprot^M
> tau_t = 0.1 0.1 ^M
> ref_t = 300 300 ^M
> ; Energy monitoring^M
> energygrps = Protein Urea_5ofprot
> ; Isotropic pressure coupling is now on^M
> Pcoupl = berendsen^M
> and at the end of the Index file i have only added the residue index of
> urea within 5 of protein and save the index file.
>
> [ Urea_5ofprot ]
> 1261 1262 1263 1264 1265 1266 1267 1268 1301 1302 1303 1304 1305 1306 1307
> 1308 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362
> 1363 1364 1413 1414 1415 1416 1417 1418 1419 1420 1501 1502 1503 1504 1505
> 1506 1507 1508 1517 1518 1519 1520 1521 1522 1523 1524 1581 1582 1583 1584
> 1585 1586 1587 1588 1637 1638 1639 1640 1641 1642 1643 1644 1685 1686 1687
> 1688 1689 1690 1691 1692 1725 1726 1727 1728 1729 1730 1731 1732 1741 1742
> 1743 1744 1745 1746 1747 1748 1773 1774 1775 1776 1777 1778 1779 1780 1781
> 1782 1783 1784 1785 1786 1787 1788 1797 1798 1799 1800 1801 1802 1803 1804
> 1893 1894 1895 1896 1897 1898 1899 1900 1933 1934 1935 1936 1937 1938 1939
> 1940 1989 1990 1991 1992 1993 1994 1995 1996 2021 2022 2023 2024 2025 2026
> 2027 2028 2253 2254 2255 2256 2257 2258 2259 2260 2269 2270 2271 2272 2273
> 2274 2275 2276 2285 2286 2287 2288 2289 2290 2291 2292 2333 2334 2335 2336
> 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2365 2366 2367
> 2368 2369 2370 2371 2372 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502
> 2503 2504 2505 2506 2507 2508 2533 2534 2535 2536 2537 2538 2539 2540 2557
> 2558 2559 2560 2561 2562 2563 2564 2621 2622 2623 2624 2625 2626 2627 2628
> 2765 2766 2767 2768 2769 2770 2771 2772 2797 2798 2799 2800 2801 2802 2803
> 2804 2901 2902 2903 2904 2905 2906 2907 2908 2917 2918 2919 2920 2921 2922
> 2923 2924 2949 2950 2951 2952 2953 2954 2955 2956 3125 3126 3127 3128 3129
> 3130 3131 3132 3237 3238 3239 3240 3241 3242 3243 3244 3325 3326 3327 3328
> 3329 3330 3331 3332 3373 3374 3375 3376 3377 3378 3379 3380 3421 3422 3423
> 3424 3425 3426 3427 3428 3477 3478 3479 3480 3481 3482 3483 3484 3541 3542
> 3543 3544 3545 3546 3547 3548 3677 3678 3679 3680 3681 3682 3683 3684 3941
> 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956
> 3973 3974 3975 3976 3977 3978 3979 3980 4117 4118 4119 4120 4121 4122 4123
> 4124 4189 4190 4191 4192 4193 4194 4195 4196 4205 4206 4207 4208 4209 4210
> 4211 4212 4245 4246 4247 4248 4249 4250 4251 4252 4333 4334 4335 4336 4337
> 4338 4339 4340 4381 4382 4383 4384 4385 4386 4387 4388 4637 4638 4639 4640
> 4641 4642 4643 4644 4669 4670 4671 4672 4673 4674 4675 4676 4701 4702 4703
> 4704 4705 4706 4707 4708 4733 4734 4735 4736 4737 4738 4739 4740 4781 4782
> 4783 4784 4785 4786 4787 4788 4861 4862 4863 4864 4865 4866 4867 4868 4893
> 4894 4895 4896 4897 4898 4899 4900 4933 4934 4935 4936 4937 4938 4939 4940
> 5021 5022 5023 5024 5025 5026 5027 5028 5085 5086 5087 5088 5089 5090 5091
> 5092 5117 5118 5119 5120 5121 5122 5123 5124 5189 5190 5191 5192 5193 5194
> 5195 5196 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257
> 5258 5259 5260 5309 5310 5311 5312 5313 5314 5315 5316 5349 5350 5351 5352
> 5353 5354 5355 5356 5373 5374 5375 5376 5377 5378 5379 5380 5453 5454 5455
> 5456 5457 5458 5459 5460 5549 5550 5551 5552 5553 5554 5555 5556 5565 5566
> 5567 5568 5569 5570 5571 5572 5581 5582 5583 5584 5585 5586 5587 5588 5669
> 5670 5671 5672 5673 5674 5675 5676 5693 5694 5695 5696 5697 5698 5699 5700
> 5813 5814 5815 5816 5817 5818 5819 5820 5901 5902 5903 5904 5905 5906 5907
> 5908 5949 5950 5951 5952 5953 5954 5955 5956 5973 5974 5975 5976 5977 5978
> 5979 5980 6005 6006 6007 6008 6009 6010 6011 6012 6061 6062 6063 6064 6065
> 6066 6067 6068 6253 6254 6255 6256 6257 6258 6259 6260 6301 6302 6303 6304
> 6305 6306 6307 6308 6333 6334 6335 6336 6337 6338 6339 6340 6373 6374 6375
> 6376 6377 6378 6379 6380 6389 6390 6391 6392 6393 6394 6395 6396 6413 6414
> 6415 6416 6417 6418 6419 6420 6485 6486 6487 6488 6489 6490 6491 6492 6517
> 6518 6519 6520 6521 6522 6523 6524 6549 6550 6551 6552 6553 6554 6555 6556
> 6573 6574 6575 6576 6577 6578 6579 6580 6629 6630 6631 6632 6633 6634 6635
> 6636 6717 6718 6719 6720 6721 6722 6723 6724 6741 6742 6743 6744 6745 6746
> 6747 6748
>
> --
> Ishrat Jahan
> Research Scholar
> Department Of Chemistry
> A.M.U Aligarh
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 07 May 2019 12:30:50 +0530
> From: spss4 at iacs.res.in
> To: gmx-users at gromacs.org
> Subject: [gmx-users] water mediated Hbond
> Message-ID:
> <20190507123050.Horde.l85d--hyr0osokDogEn6AsF at mailweb.iacs.res.in>
> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
>
> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecule. What extra flag should I use in gmx hbond command? Is
> there any other option to capture the water mediated Hbonds? Please
> suggest something.
> Sunipa Sarkar
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 7 May 2019 09:14:42 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] GROMOS 54A8 Force field
> Message-ID:
> <CAMNuMASUNWd=VQ3qJQNK5KD03O-Uib=
> Vd6W5wECjfEjgVXmYcQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I would contact the authors and ask them.
>
> Mark
>
Dear Mark,
Thank you very much for your suggestion.
Sincerely yours,
Kalyanashis Jana
>
> On Mon, 6 May 2019 at 11:30, Kalyanashis Jana <kalyan.chem.in at gmail.com>
> wrote:
>
> > Dear users,
> > Could you please suggest me where I can get the complete package of
> GROMOS
> > 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker (
> > https://pubs.acs.org/doi/10.1021/ct300156h).
> >
> > Looking forward to your suggestions.
> >
> > Thanks in advance.
> >
> > Sincerely yours,
> > Kalyanashis Jana
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> >
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 7 May 2019 09:14:42 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] GROMOS 54A8 Force field
> Message-ID:
> <CAMNuMASUNWd=VQ3qJQNK5KD03O-Uib=
> Vd6W5wECjfEjgVXmYcQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I would contact the authors and ask them.
>
> Mark
>
> On Mon, 6 May 2019 at 11:30, Kalyanashis Jana <kalyan.chem.in at gmail.com>
> wrote:
>
> > Dear users,
> > Could you please suggest me where I can get the complete package of
> GROMOS
> > 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker (
> > https://pubs.acs.org/doi/10.1021/ct300156h).
> >
> > Looking forward to your suggestions.
> >
> > Thanks in advance.
> >
> > Sincerely yours,
> > Kalyanashis Jana
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 7 May 2019 09:16:06 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Error when compiling 2019.2 with -DGMX_MPI=ON
> Message-ID:
> <CAMNuMAQ8-g=ZiSvM4871AEv4a=
> 9HdfG0Ga8MZDa+YR-5t1mruw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Dallas,
>
> The install guide tries to provide the hint to use the MPI wrapper
> compilers (mpicc and mpicxx) that are installed alongside the MPI package
> you installed (but maybe as part of the *mpi-dev package) . Perhaps we can
> make that more clear. (And if you do, there's no need to set GMX_MPI, as
> the build system will see what your intent is.) The symptoms you report
> look very much like those that mpicc will handle internally.
> Mark
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
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> End of gromacs.org_gmx-users Digest, Vol 181, Issue 14
> ******************************************************
>
--
With best regards
Kalyanashis Jana
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