Make it easy with ORCA Pada tanggal 14 Jun 2016 05.19, "Clinton King" <[email protected]> menulis:
> Gerrit, > > Thanks for your suggestions. I am using GROMACS 5.1.2. > > After reading through your message, I realized that I was using GAUSS_DIR > and GAUSS_EXE for the location and name of the gau script instead of > GMX_QM_GAUSS_DIR and GMX_QM_GAUSS_EXE. So I changed that, and then I got > the error message from line 227 of qm_gaussian.c : "no > $GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside." > > I thought that one could use the gau script successfully without modifying > any Gaussian links. > > I decided to try setting the GMX_QM_MODIFIED_LINKS_DIR environmental > variable to an empty folder. I am attaching the resulting output (as links > at the end of this message); both what was sent to stdout as well as the > gmx generated log file. > > Looking through qm_gaussian.c, as well as the output I have so far, it > appears that modified Gaussian links *are* required for gmx to interface > with Gaussian. > > So, the bottom line is that in order for Gromacs to interface with Gaussian > to perform a quantum molecular dynamics computation, I must have access to > the Gaussian source code. Is that correct? > > > https://drive.google.com/file/d/0B-W4G39j_Icjc21TcTN1S2M0MVk/view?usp=sharing > > https://drive.google.com/file/d/0B-W4G39j_IcjZlVPb1NySkUtRDQ/view?usp=sharing > > (Please let me know if the links above don't work.) > > Thanks for your help > > -- > Clinton King > Graduate Student > Chemistry Department > Brigham Young University > > > > Message: 2 > > Date: Sun, 12 Jun 2016 05:16:13 +0000 > > From: "Groenhof, Gerrit" <[email protected]> > > To: "[email protected]" > > <[email protected]> > > Subject: Re: [gmx-users] interfacing with Gaussian 09 (Mark Abraham) > > Message-ID: > > < > 858a7947bc0fe04da05e1786a6d51d45263d6...@um-excdag-a05.um.gwdg.de > > > > > Content-Type: text/plain; charset="us-ascii" > > > > Hi, > > > > Which version of Gmx are you using? > > > > I ask because of a recent bug fix. The bug was that I tried to print the > > value of an environment variable, without checking if that variable was > > set, causing set faulting. > > > > Make sure the GMX_QM_GAUSS_DIR (for Gmx < 5 GAUSS_DIR) are set and point > > to the location of the g09 directory. > > > > IN any case, for normal gaussian runs, the program should not write out > > the LJ.dat. IF the above does not help, you could perhaps send me the > input > > (off list) and I can have a look at what goes wrong. > > > > Best, > > > > Gerrit > > > > > > > > Hi, > > > > Please don't subscribe to a digest if you're planning to reply to the > > digest and de-thread the discussion. Gerrit said the other week that gau > > works. > > > > Mark > > > > On Fri, 10 Jun 2016 18:18 Mark Abraham <[email protected]> wrote: > > > > > Hi, > > > > > > Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and > > > > > > http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM > > > > > > Mark > > > > > > On Fri, Jun 10, 2016 at 5:13 PM Clinton King < > [email protected] > > > > > > wrote: > > > > > >> I'm having difficulty interfacing GROMACS with Gaussian 09. Is there > > >> anyone > > >> who has successfully done it who is willing to give some advice? > > >> > > >> -- > > >> Clinton King > > >> Graduate Student > > >> Chemistry Department > > >> Brigham Young University > > >> -- > > >> 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 [email protected]. > > >> > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 10 Jun 2016 14:27:01 -0600 > > From: Clinton King <[email protected]> > > To: [email protected] > > Subject: Re: [gmx-users] interfacing with Gaussian 09 > > Message-ID: > > <CABUMFLJBjWOgKGW0qUNFasGHUm_52f1k_RbHX=_ > > [email protected]> > > Content-Type: text/plain; charset=UTF-8 > > > > Sorry I forgot to change the subject line on my previous message; it was > > inadvertent. If Gerrit gets these emails maybe he can tell me what I'm > > doing wrong. Here are the symptoms: > > > > I'm using the gau script and I think the program is executing through > until > > at least line 177 of the qm_gaussian.c code, as I see the message, "Level > > of SA at start = %d\n" in the output. However, soon after that, the > process > > terminates with a segmentation fault. I think it is terminating before > line > > 184 in the same code, as I don't believe the file LJ.dat is ever created. > > > > Maybe this means that the program isn't even getting to the point in > which > > it calls up the gau script which in turn calls up Gaussian, since that > > happens on line 214 of the gm_gaussian.c code? > > > > Thanks in advance for any help anyone can offer.. > > > > Clinton > > > > > > > > > -- > 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 [email protected]. > -- 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 [email protected].
