Hi,
O'right, I will take a closer look.
Thank you!
2015-08-10 10:11 GMT+01:00 Mark Abraham :
> Hi,
>
> OK, that sounds good. I ran your speedyshare files just fine with 4.6.7, so
> I think you are not using the files you think you are using.
>
> Mark
>
> On Mon, Aug 10, 2015 at 10:30 AM Dawid da
Hi,
OK, that sounds good. I ran your speedyshare files just fine with 4.6.7, so
I think you are not using the files you think you are using.
Mark
On Mon, Aug 10, 2015 at 10:30 AM Dawid das wrote:
> Well, the *itp file says:
>
> #ifdef FLEXIBLE
>
> and there is bunch of lines defining proper pa
Well, the *itp file says:
#ifdef FLEXIBLE
and there is bunch of lines defining proper parameters, so I assumed this
is it.
2015-08-10 6:26 GMT+01:00 Mark Abraham :
> You've *tried* to use flexible water. But does your water itp file *have* a
> flexible implementation that your approach will tri
You've *tried* to use flexible water. But does your water itp file *have* a
flexible implementation that your approach will trigger?
Mark
On Sun, 9 Aug 2015 19:42 Dawid das wrote:
> 2015-08-09 18:27 GMT+01:00 Mark Abraham :
>
> >
> > Justin's advice is true only if your water topology has a fle
2015-08-09 18:25 GMT+01:00 Justin Lemkul :
> Are you using some old version? Note that your cutoff setup is wrong for
> CHARMM force fields.
Well, to be honest I do use quite and old version which is 4.6.7.
Yes I am aware of that I use wrong CHARMM force field cutoff setup and
values.
I have do
2015-08-09 18:27 GMT+01:00 Mark Abraham :
>
> Justin's advice is true only if your water topology has a flexible
> implementation. Check it
Yes, I do use flexible water and still this causes problem.
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Hi,
Justin's advice is true only if your water topology has a flexible
implementation. Check it.
Mark
On Sun, 9 Aug 2015 17:41 Dawid das wrote:
> Dear Justin,
>
> I still have problems with performing l-bfgs minimization.
> I use
>
> constraints = none ; no constraints
> define
On 8/9/15 1:17 PM, Dawid das wrote:
I hope speedy share is fine.
http://www.speedyshare.com/k2YEr/ribonucl-no-constr.tar.gz
Works for me with the latest GROMACS. Are you using some old version? Note
that your cutoff setup is wrong for CHARMM force fields. See
http://www.gromacs.org/Doc
I hope speedy share is fine.
http://www.speedyshare.com/k2YEr/ribonucl-no-constr.tar.gz
2015-08-09 18:08 GMT+01:00 Justin Lemkul :
>
>
> On 8/9/15 11:40 AM, Dawid das wrote:
>
>> Dear Justin,
>>
>> I still have problems with performing l-bfgs minimization.
>> I use
>>
>> constraints
On 8/9/15 11:40 AM, Dawid das wrote:
Dear Justin,
I still have problems with performing l-bfgs minimization.
I use
constraints = none ; no constraints
define = -DFLEXIBLE
in my *mdp file and in *top file there is nothing related to constraints.
I still get this
Dear Justin,
I still have problems with performing l-bfgs minimization.
I use
constraints = none ; no constraints
define = -DFLEXIBLE
in my *mdp file and in *top file there is nothing related to constraints.
I still get this error that l-bfgs and constraints are no
2015-07-29 12:36 GMT+01:00 Justin Lemkul :
> To turn that off you would need "define = -DFLEXIBLE" but you should
> subsequently re-minimize with constraints to avoid weird geometries.
I forgot about it. Thank you!
Dawid Grabarek
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On 7/29/15 7:30 AM, Dawid das wrote:
Dear Gromacs Experts,
I am trying to run l-bfgs minimization with following options (apart from
others):
integrator = l-bfgs ; (other: cg, l-bfgs)
constraints = none ; no constraints
but I still get a message that l-bfgs does no
Dear Gromacs Experts,
I am trying to run l-bfgs minimization with following options (apart from
others):
integrator = l-bfgs ; (other: cg, l-bfgs)
constraints = none ; no constraints
but I still get a message that l-bfgs does not work with constraints so I
should eithe
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