Re: [AMBER] XMIN internal output suppressed

From: Istvan Kolossvary <>
Date: Wed, 20 Feb 2019 22:19:00 -0500


I am all for the C interface. Does it provide access to the NMR restraint module? My reason to switch to sander was applying restraints. I noticed that LMOD tests were disabled in the sander test suite, it may not have been used for a while. I could, of course write a simple NOE module in C and that may be the best solution.



> On Feb 20, 2019, at 9:03 PM, David Case <> wrote:
>> On Wed, Feb 20, 2019, Istvan Kolossvary wrote:
>> I am trying to migrate XMIN/LMOD nab scripts working with sander. With
>> XMIN I see significant differences between nab and sander and would like
>> to check internal debugging output to find out more about it. I
>> understand that XMIN internal output can be confusing mixed with sander
>> output, but I need it for debugging. However, setting xmin_verbosity > 0
>> in the &xmin.../ block does not seem to have any effect, I cannot see
>> any internal XMIN output, only the standard sander minimization output.
>> Is this intentional or have I overlooked something?
> It's not intentional, but would take some code exploration to figure out
> what is happening. I don't remember anything about this.
> It would be good to track down, since we certainly expect the sff results
> to be the same as those from sander. However, (personal bias showing
> here:) have you considered migrating from NAB to C? For a gas-phase
> (or GB solvent) problem like you show below, a C-driver linked to sff
> should be simpler, faster, more portable and more parallelizable, than the
> corresponding sander code. Of course, you'll need sander if your ulitmate
> targets involve QM/MM or periodic systems.
> Sorry to not be of much help here.
> ....dac
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Received on Wed Feb 20 2019 - 19:30:03 PST
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