[gmx-users] Problems with large molecule simulation

[Justin Lemkul]

On 5/16/17 1:32 PM, Tam, Benjamin wrote:
> Hi Justin,
>
> Thank you for replying, the problem is this:
>
> Fatal error:
> Atomtype Zr110418 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> because the number and the name combine together i.e. supposed to be Zr1 10418. How can I solve this problem?
>

That error is coming from the topology, not the coordinate file.

-Justin

> Best regards,
>
> Ben
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
> Sent: 16 May 2017 18:30
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problems with large molecule simulation
>
>
>
> On 5/16/17 1:27 PM, Ben Tam wrote:
>>
>> Dear gromacs user,
>>
>> I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count:
>>
>>     2MOL     C2 9998   3.987   2.259   6.276
>>     2MOL     C5 9999   3.987   2.061   6.079
>>     2MOL     C110000   3.987   1.025   7.721
>>     2MOL     C210001   3.987   0.920   7.615
>>
>> Sorry for this basic question, but how do people solve that problem? As I know there is a specific format for .gro file?
>>
>
> Yes, it is fixed-format.
>
> http://manual.gromacs.org/documentation/2016.3/user-guide/file-formats.html#gro
>
> What exactly is the nature of the problem?  Most common systems are >10k atoms and all GROMACS tools should handle things just fine.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================