Re: [gmx-users] LINCS warning during constrained md

[edesantis]

Dear Mark,
I understand your point,
but I've used the Martini-backmapping protocol written in the initram.sh 
wrapper found in Martini documentation 
(https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it 
seems to me quite weird that it was not working in the proper manner.



an other problem is that I've to convert some thousands of structure 
extracted from the martini trajectory,
I thought that this kind of conversion doesn't require to much effort, 
so for this reason I thought that the posres flag was useful to limit 
the computational time... maybe I'm wrong


Can I avoid to use constrained bonds and use only posres? what do you 
think about?




in addition, for you, how many steps of md have I to perform to do this 
kind of equilibration? have I to look necessarily at the rmsd in each 
trajectory? I'd like to have a robust protocol to do all the conversions 
in an automatic way...


thank you again for your suggestions
regards,
Emiliano



On 2017-07-12 17:23, Mark Abraham wrote:

Hi,

I would avoid using the combination of position restraints and 
constrained
bonds with an input structure that is not necessarily consistent with 
the

constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that 
my
starting structure was special *and* saw a large deformation if I 
didn't
use the restraints. If I saw the deformation, I would wonder why I 
thought

it was special.

If you're trying to relax a thing, let it relax. :-) If something 
strange
happens, consider that when it has happened. Obviously that means you 
want
to look at what happens when you did your equilibration, but you were 
going

to do that anyway. Right? ;-)

Mark

On Wed, Jul 12, 2017 at 5:17 PM edesantis  
wrote:



hi,

I've seen with vmd the gro file generated after the transformation, 
and

after the 2 steps of minimization,
it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there 
are

some atoms far away from the rest of the protein, while this is not
happening if I comment the restrains part


do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:
> Hi,
>
> Those are all good things, but have you actually got out a molecular
> viewer
> and looked at the input and output of your resolution conversion?
>
> Mark
>
> On Wed, Jul 12, 2017 at 4:25 PM edesantis 
> wrote:
>
>> Hi,
>> thanks for the prompt answer,
>>
>>
>> I've found the same problem even if I try to convert the coarse
>> grained
>> pdb obtained from martinize.py, so in that case it should be not a
>> problem to have the conversion, for this reason I though it is a
>> methodological problem...
>>
>> I've seen the blowing-up issues , but I think:
>> - the timestep is enough small  (0.0002)
>> -the system should be enough minimized via the previous steps (in fact
>> the sd converged to the machine precision in both cases, actually the
>> potential energy is ~10^5, but I don't know how to reduce it, I tried
>> a
>> cg after the sd, but the proble is still there)
>> -there in not any pressure coupling
>> -I've tried a different temperature coupling (berensden, nose-hoover)
>> and it doesn't work
>> - the md stops at the first step, so there is not any .edr file
>> produced
>> to be looked at
>>
>>
>>
>> I don't know what else to do...
>>
>> maybe, do you know another conversion protocol to use??
>>
>>
>> thank you again
>> Emiliano
>>
>> On 2017-07-12 15:11, Mark Abraham wrote:
>> > Hi,
>> >
>> > Sounds like you might be
>> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because
the
>> > conversion doesn't work for your configuration. You should start by
>> > doing a
>> > visual check of the configuration for sanity, then follow the advice
in
>> > that link.
>> >
>> > Mark
>> >
>> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
>> > wrote:
>> >
>> >> dear all,
>> >>
>> >> I am facing a problem with the conversion from Martini CG
>> >> representation
>> >> to All-atomistic one.
>> >>
>> >> I am using the initram.sh wrapper around the backward.py.
>> >>
>> >> There is a LINCS warning problem when the energy relaxation is
>> >> performed
>> >> using position restrained md
>> >> (I've also tried to run grompp and mdrun commands directly from the
>> >> terminal and the error persists, so it is not a wrapper problem).
>> >>
>> >> this is the .mdp file generated by the script:
>> >>
>> >> "define   = -DPOSRES
>> >> integrator   = md
>> >> nsteps   = 500
>> >> dt   = 0.0002
>> >> pbc  = xyz
>> >>
>> >> rcoulomb = 0.9
>> >> rlist= 0.9
>> >> rvdw = 0.9
>> >>
>> >> tcoupl   = v-rescale
>> >> ref_t= 200
>> >> tau_t= 0.1
>> >> 

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

I would avoid using the combination of position restraints and constrained
bonds with an input structure that is not necessarily consistent with the
constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that my
starting structure was special *and* saw a large deformation if I didn't
use the restraints. If I saw the deformation, I would wonder why I thought
it was special.

If you're trying to relax a thing, let it relax. :-) If something strange
happens, consider that when it has happened. Obviously that means you want
to look at what happens when you did your equilibration, but you were going
to do that anyway. Right? ;-)

Mark

On Wed, Jul 12, 2017 at 5:17 PM edesantis  wrote:

> hi,
>
> I've seen with vmd the gro file generated after the transformation, and
> after the 2 steps of minimization,
> it seems that they have no problem,
> while if I see the step_n.pdb file generated before the crash, there are
> some atoms far away from the rest of the protein, while this is not
> happening if I comment the restrains part
>
>
> do you understand why??
>
> thank you again,
> Emiliano
>
>
>
> On 2017-07-12 16:29, Mark Abraham wrote:
> > Hi,
> >
> > Those are all good things, but have you actually got out a molecular
> > viewer
> > and looked at the input and output of your resolution conversion?
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 4:25 PM edesantis 
> > wrote:
> >
> >> Hi,
> >> thanks for the prompt answer,
> >>
> >>
> >> I've found the same problem even if I try to convert the coarse
> >> grained
> >> pdb obtained from martinize.py, so in that case it should be not a
> >> problem to have the conversion, for this reason I though it is a
> >> methodological problem...
> >>
> >> I've seen the blowing-up issues , but I think:
> >> - the timestep is enough small  (0.0002)
> >> -the system should be enough minimized via the previous steps (in fact
> >> the sd converged to the machine precision in both cases, actually the
> >> potential energy is ~10^5, but I don't know how to reduce it, I tried
> >> a
> >> cg after the sd, but the proble is still there)
> >> -there in not any pressure coupling
> >> -I've tried a different temperature coupling (berensden, nose-hoover)
> >> and it doesn't work
> >> - the md stops at the first step, so there is not any .edr file
> >> produced
> >> to be looked at
> >>
> >>
> >>
> >> I don't know what else to do...
> >>
> >> maybe, do you know another conversion protocol to use??
> >>
> >>
> >> thank you again
> >> Emiliano
> >>
> >> On 2017-07-12 15:11, Mark Abraham wrote:
> >> > Hi,
> >> >
> >> > Sounds like you might be
> >> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because
> the
> >> > conversion doesn't work for your configuration. You should start by
> >> > doing a
> >> > visual check of the configuration for sanity, then follow the advice
> in
> >> > that link.
> >> >
> >> > Mark
> >> >
> >> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> >> > wrote:
> >> >
> >> >> dear all,
> >> >>
> >> >> I am facing a problem with the conversion from Martini CG
> >> >> representation
> >> >> to All-atomistic one.
> >> >>
> >> >> I am using the initram.sh wrapper around the backward.py.
> >> >>
> >> >> There is a LINCS warning problem when the energy relaxation is
> >> >> performed
> >> >> using position restrained md
> >> >> (I've also tried to run grompp and mdrun commands directly from the
> >> >> terminal and the error persists, so it is not a wrapper problem).
> >> >>
> >> >> this is the .mdp file generated by the script:
> >> >>
> >> >> "define   = -DPOSRES
> >> >> integrator   = md
> >> >> nsteps   = 500
> >> >> dt   = 0.0002
> >> >> pbc  = xyz
> >> >>
> >> >> rcoulomb = 0.9
> >> >> rlist= 0.9
> >> >> rvdw = 0.9
> >> >>
> >> >> tcoupl   = v-rescale
> >> >> ref_t= 200
> >> >> tau_t= 0.1
> >> >> tc_grps  = System
> >> >>
> >> >> gen_vel  = yes
> >> >> gen_temp = 300
> >> >>
> >> >> constraints  = all-bonds "
> >> >>
> >> >>
> >> >> this is the error I found in the .log file:
> >> >>
> >> >> "Fatal error:
> >> >> Too many LINCS warnings (1034)
> >> >> If you know what you are doing you can adjust the lincs warning
> >> >> threshold in your mdp file
> >> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
> >> >> but normally it is better to fix the problem "
> >> >>
> >> >> I tired to comment the constrains part and all is working, but since
> >> >> the
> >> >> structure should not be altered too much, I think the constraints are
> >> >> required (if I constrain only the h-bonds, it is also working).
> >> >>
> >> >> I've also added to the .mdp 

Re: [gmx-users] LINCS warning during constrained md

[edesantis]

hi,

I've seen with vmd the gro file generated after the transformation, and 
after the 2 steps of minimization,

it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there are 
some atoms far away from the rest of the protein, while this is not 
happening if I comment the restrains part



do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:

Hi,

Those are all good things, but have you actually got out a molecular 
viewer

and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis  
wrote:



Hi,
thanks for the prompt answer,


I've found the same problem even if I try to convert the coarse 
grained

pdb obtained from martinize.py, so in that case it should be not a
problem to have the conversion, for this reason I though it is a
methodological problem...

I've seen the blowing-up issues , but I think:
- the timestep is enough small  (0.0002)
-the system should be enough minimized via the previous steps (in fact
the sd converged to the machine precision in both cases, actually the
potential energy is ~10^5, but I don't know how to reduce it, I tried 
a

cg after the sd, but the proble is still there)
-there in not any pressure coupling
-I've tried a different temperature coupling (berensden, nose-hoover)
and it doesn't work
- the md stops at the first step, so there is not any .edr file 
produced

to be looked at



I don't know what else to do...

maybe, do you know another conversion protocol to use??


thank you again
Emiliano

On 2017-07-12 15:11, Mark Abraham wrote:
> Hi,
>
> Sounds like you might be
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
> conversion doesn't work for your configuration. You should start by
> doing a
> visual check of the configuration for sanity, then follow the advice in
> that link.
>
> Mark
>
> On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> wrote:
>
>> dear all,
>>
>> I am facing a problem with the conversion from Martini CG
>> representation
>> to All-atomistic one.
>>
>> I am using the initram.sh wrapper around the backward.py.
>>
>> There is a LINCS warning problem when the energy relaxation is
>> performed
>> using position restrained md
>> (I've also tried to run grompp and mdrun commands directly from the
>> terminal and the error persists, so it is not a wrapper problem).
>>
>> this is the .mdp file generated by the script:
>>
>> "define   = -DPOSRES
>> integrator   = md
>> nsteps   = 500
>> dt   = 0.0002
>> pbc  = xyz
>>
>> rcoulomb = 0.9
>> rlist= 0.9
>> rvdw = 0.9
>>
>> tcoupl   = v-rescale
>> ref_t= 200
>> tau_t= 0.1
>> tc_grps  = System
>>
>> gen_vel  = yes
>> gen_temp = 300
>>
>> constraints  = all-bonds "
>>
>>
>> this is the error I found in the .log file:
>>
>> "Fatal error:
>> Too many LINCS warnings (1034)
>> If you know what you are doing you can adjust the lincs warning
>> threshold in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem "
>>
>> I tired to comment the constrains part and all is working, but since
>> the
>> structure should not be altered too much, I think the constraints are
>> required (if I constrain only the h-bonds, it is also working).
>>
>> I've also added to the .mdp file the lines:
>> " lincs-order  = 4 (or 2 or 8)
>> lincs-iter   = 1 (or 2 or 10)
>> "
>> but it is still not working...
>>
>>
>> any of you have suggestions to solve the problem??
>> how is it possible to change the environment variable?
>>
>>
>> thanks in advance for your help
>> Emiliano
>>
>> --
>> Emiliano De Santis
>>
>> --
>> 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-requ...@gromacs.org.
>>

--
Emiliano De Santis
--
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-requ...@gromacs.org.



--
Emiliano De Santis
--
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

* 

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Those are all good things, but have you actually got out a molecular viewer
and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis  wrote:

> Hi,
> thanks for the prompt answer,
>
>
> I've found the same problem even if I try to convert the coarse grained
> pdb obtained from martinize.py, so in that case it should be not a
> problem to have the conversion, for this reason I though it is a
> methodological problem...
>
> I've seen the blowing-up issues , but I think:
> - the timestep is enough small  (0.0002)
> -the system should be enough minimized via the previous steps (in fact
> the sd converged to the machine precision in both cases, actually the
> potential energy is ~10^5, but I don't know how to reduce it, I tried a
> cg after the sd, but the proble is still there)
> -there in not any pressure coupling
> -I've tried a different temperature coupling (berensden, nose-hoover)
> and it doesn't work
> - the md stops at the first step, so there is not any .edr file produced
> to be looked at
>
>
>
> I don't know what else to do...
>
> maybe, do you know another conversion protocol to use??
>
>
> thank you again
> Emiliano
>
> On 2017-07-12 15:11, Mark Abraham wrote:
> > Hi,
> >
> > Sounds like you might be
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
> > conversion doesn't work for your configuration. You should start by
> > doing a
> > visual check of the configuration for sanity, then follow the advice in
> > that link.
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> > wrote:
> >
> >> dear all,
> >>
> >> I am facing a problem with the conversion from Martini CG
> >> representation
> >> to All-atomistic one.
> >>
> >> I am using the initram.sh wrapper around the backward.py.
> >>
> >> There is a LINCS warning problem when the energy relaxation is
> >> performed
> >> using position restrained md
> >> (I've also tried to run grompp and mdrun commands directly from the
> >> terminal and the error persists, so it is not a wrapper problem).
> >>
> >> this is the .mdp file generated by the script:
> >>
> >> "define   = -DPOSRES
> >> integrator   = md
> >> nsteps   = 500
> >> dt   = 0.0002
> >> pbc  = xyz
> >>
> >> rcoulomb = 0.9
> >> rlist= 0.9
> >> rvdw = 0.9
> >>
> >> tcoupl   = v-rescale
> >> ref_t= 200
> >> tau_t= 0.1
> >> tc_grps  = System
> >>
> >> gen_vel  = yes
> >> gen_temp = 300
> >>
> >> constraints  = all-bonds "
> >>
> >>
> >> this is the error I found in the .log file:
> >>
> >> "Fatal error:
> >> Too many LINCS warnings (1034)
> >> If you know what you are doing you can adjust the lincs warning
> >> threshold in your mdp file
> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
> >> but normally it is better to fix the problem "
> >>
> >> I tired to comment the constrains part and all is working, but since
> >> the
> >> structure should not be altered too much, I think the constraints are
> >> required (if I constrain only the h-bonds, it is also working).
> >>
> >> I've also added to the .mdp file the lines:
> >> " lincs-order  = 4 (or 2 or 8)
> >> lincs-iter   = 1 (or 2 or 10)
> >> "
> >> but it is still not working...
> >>
> >>
> >> any of you have suggestions to solve the problem??
> >> how is it possible to change the environment variable?
> >>
> >>
> >> thanks in advance for your help
> >> Emiliano
> >>
> >> --
> >> Emiliano De Santis
> >>
> >> --
> >> 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-requ...@gromacs.org.
> >>
>
> --
> Emiliano De Santis
> --
> 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-requ...@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-requ...@gromacs.org.

Re: [gmx-users] LINCS warning during constrained md

[edesantis]

Hi,
thanks for the prompt answer,


I've found the same problem even if I try to convert the coarse grained 
pdb obtained from martinize.py, so in that case it should be not a 
problem to have the conversion, for this reason I though it is a 
methodological problem...


I've seen the blowing-up issues , but I think:
- the timestep is enough small  (0.0002)
-the system should be enough minimized via the previous steps (in fact 
the sd converged to the machine precision in both cases, actually the 
potential energy is ~10^5, but I don't know how to reduce it, I tried a 
cg after the sd, but the proble is still there)

-there in not any pressure coupling
-I've tried a different temperature coupling (berensden, nose-hoover) 
and it doesn't work
- the md stops at the first step, so there is not any .edr file produced 
to be looked at




I don't know what else to do...

maybe, do you know another conversion protocol to use??


thank you again
Emiliano

On 2017-07-12 15:11, Mark Abraham wrote:

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by 
doing a

visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis  
wrote:



dear all,

I am facing a problem with the conversion from Martini CG 
representation

to All-atomistic one.

I am using the initram.sh wrapper around the backward.py.

There is a LINCS warning problem when the energy relaxation is 
performed

using position restrained md
(I've also tried to run grompp and mdrun commands directly from the
terminal and the error persists, so it is not a wrapper problem).

this is the .mdp file generated by the script:

"define   = -DPOSRES
integrator   = md
nsteps   = 500
dt   = 0.0002
pbc  = xyz

rcoulomb = 0.9
rlist= 0.9
rvdw = 0.9

tcoupl   = v-rescale
ref_t= 200
tau_t= 0.1
tc_grps  = System

gen_vel  = yes
gen_temp = 300

constraints  = all-bonds "


this is the error I found in the .log file:

"Fatal error:
Too many LINCS warnings (1034)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem "

I tired to comment the constrains part and all is working, but since 
the

structure should not be altered too much, I think the constraints are
required (if I constrain only the h-bonds, it is also working).

I've also added to the .mdp file the lines:
" lincs-order  = 4 (or 2 or 8)
lincs-iter   = 1 (or 2 or 10)
"
but it is still not working...


any of you have suggestions to solve the problem??
how is it possible to change the environment variable?


thanks in advance for your help
Emiliano

--
Emiliano De Santis

--
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-requ...@gromacs.org.



--
Emiliano De Santis
--
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-requ...@gromacs.org.

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by doing a
visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis  wrote:

> dear all,
>
> I am facing a problem with the conversion from Martini CG representation
> to All-atomistic one.
>
> I am using the initram.sh wrapper around the backward.py.
>
> There is a LINCS warning problem when the energy relaxation is performed
> using position restrained md
> (I've also tried to run grompp and mdrun commands directly from the
> terminal and the error persists, so it is not a wrapper problem).
>
> this is the .mdp file generated by the script:
>
> "define   = -DPOSRES
> integrator   = md
> nsteps   = 500
> dt   = 0.0002
> pbc  = xyz
>
> rcoulomb = 0.9
> rlist= 0.9
> rvdw = 0.9
>
> tcoupl   = v-rescale
> ref_t= 200
> tau_t= 0.1
> tc_grps  = System
>
> gen_vel  = yes
> gen_temp = 300
>
> constraints  = all-bonds "
>
>
> this is the error I found in the .log file:
>
> "Fatal error:
> Too many LINCS warnings (1034)
> If you know what you are doing you can adjust the lincs warning
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem "
>
> I tired to comment the constrains part and all is working, but since the
> structure should not be altered too much, I think the constraints are
> required (if I constrain only the h-bonds, it is also working).
>
> I've also added to the .mdp file the lines:
> " lincs-order  = 4 (or 2 or 8)
> lincs-iter   = 1 (or 2 or 10)
> "
> but it is still not working...
>
>
> any of you have suggestions to solve the problem??
> how is it possible to change the environment variable?
>
>
> thanks in advance for your help
> Emiliano
>
> --
> Emiliano De Santis
>
> --
> 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-requ...@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-requ...@gromacs.org.

[gmx-users] LINCS warning during constrained md

[edesantis]

dear all,

I am facing a problem with the conversion from Martini CG representation 
to All-atomistic one.


I am using the initram.sh wrapper around the backward.py.

There is a LINCS warning problem when the energy relaxation is performed 
using position restrained md
(I've also tried to run grompp and mdrun commands directly from the 
terminal and the error persists, so it is not a wrapper problem).


this is the .mdp file generated by the script:

"define   = -DPOSRES
integrator   = md
nsteps   = 500
dt   = 0.0002
pbc  = xyz

rcoulomb = 0.9
rlist= 0.9
rvdw = 0.9

tcoupl   = v-rescale
ref_t= 200
tau_t= 0.1
tc_grps  = System

gen_vel  = yes
gen_temp = 300

constraints  = all-bonds "


this is the error I found in the .log file:

"Fatal error:
Too many LINCS warnings (1034)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem "

I tired to comment the constrains part and all is working, but since the 
structure should not be altered too much, I think the constraints are 
required (if I constrain only the h-bonds, it is also working).


I've also added to the .mdp file the lines:
" lincs-order  = 4 (or 2 or 8)
lincs-iter   = 1 (or 2 or 10)
"
but it is still not working...


any of you have suggestions to solve the problem??
how is it possible to change the environment variable?


thanks in advance for your help
Emiliano

--
Emiliano De Santis

--
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-requ...@gromacs.org.