[gmx-users] custom force constants

[Irem Altan]

Hi,

I can’t believe I overlooked something that simple. Thanks!

Best,
Irem

> On Jan 20, 2016, at 10:19 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> Table 5.5. of the manual shows the required formats - and the hint in the
> comment in your file is accurate also. You need to specify a "type" field
> (often 1).
> 
> Mark
> 
> On Wed, Jan 20, 2016 at 4:11 PM Irem Altan <irem.altan at duke.edu> wrote:
> 
>> Hi,
>> 
>> I am trying to create a position restraint file with custom force
>> constants. The file looks like as follows:
>> 
>> ; In this topology include file, you will find position restraint
>> ; entries for all the heavy atoms in your original pdb file.
>> ; This means that all the protons which were added by pdb2gmx are
>> ; not restrained.
>> 
>> [ position_restraints ]
>> ; atom  type      fx      fy      fz
>> 1 2271 2271 2271
>> 5 2202 2202 2202
>> 7 2160 2160 2160
>> 10 2523 2523 2523
>> 
>> etc.
>> 
>> However, when I’m trying to create an executable with grompp, I get the
>> following error:
>> 
>> Fatal error:
>> Invalid position restraint type 2271
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> The documentation does not list this error as far as I can see. Does this
>> mean that intermediate values are not allowed? If so, what are the allowed
>> values and what do they correspond to?
>> 
>> Best,
>> Irem
>> --
>> 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.
> -- 
> 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.