subject:"\[gmx\-users\] mdrun error"

[gmx-users] mdrun error

2019-09-10 Thread KRISHNA PRASAD GHANTA

Hi gromacs user

I am simulating protein ionic liquid(IL) system, in my IL forcefield the
function type of dihedral parameter is 5. When I am running
gmx mdrun it appears the following error.


Program: gmx mdrun, version 2018.1
Source file: src/gromacs/topology/topsort.cpp (line 139)

Fatal error:
Function type Fourier Dih. not implemented in ip_pert

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

After getting this error I have used function type 3 that also showed
Ryckaert-Bellemans dihedral error
Any suggestion will be appreciated to resolve this problem.

**

*Krishna Prasad GhantaResearch Scholar*
*Molecular Modeling Laboratory*
*Indian Institute Of Technology Kharagpur*


*Kharagpur-721302Contact no - 8327297650*
***
-- 
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] mdrun error

2019-09-01 Thread Justin Lemkul




On 9/1/19 7:02 AM, m g wrote:

Dear Justin,

There are many other people on this list, and I don't always have answers :)


  I'm simulating a system with "wall" for z direction, but I gave this error in 
minimization step "software inconsistency error: lost particles while sorting",.Would you 
please help me? I used the following parameter:


What GROMACS version are you using? CPU or GPU? Does the simulation work 
without the walls? You need to provide a lot more diagnostic 
information. This is a cryptic error that suggests something very 
fundamental is wrong. That also makes it very hard to diagnose.


If you're not using the latest version of GROMACS, start there. I recall 
some bug fixes that may be relevant. If the error is reproducible in 
2019.3, please post a more complete description of what you're doing.


-Justin


integrator      =steep

emtol       = 100.0emstep  = 0.01nsteps        = 
5000nstlist       = 1cutoff-scheme   = Verletns_type       
= gridrlist       = 1.2    coulombtype     = PMErcoulomb        
= 1.2vdwtype = cutoffvdw-modifier    = force-switchrvdw-switch  
   = 1.0rvdw        = 1.2    DispCorr    = nopbc    
 =xy                    nwall   = 2wall_type   
= 10-4wall_r_linpot   = 1wall_atomtype   = ca  cawall_density    = 
60  60wall_ewald_zfac = 3ewald-geometry  = 3dc

Thanks,Ganj



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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] mdrun error

2019-09-01 Thread m g

Dear Justin, I'm simulating a system with "wall" for z direction, but I gave 
this error in minimization step "software inconsistency error: lost particles 
while sorting",.Would you please help me? I used the following parameter:

integrator      =steep   

emtol       = 100.0emstep  = 0.01nsteps        = 
5000nstlist       = 1cutoff-scheme   = Verletns_type       
= gridrlist       = 1.2    coulombtype     = PMErcoulomb        
= 1.2vdwtype = cutoffvdw-modifier    = force-switchrvdw-switch  
   = 1.0rvdw        = 1.2    DispCorr    = nopbc    
 =xy                    nwall   = 2wall_type   
= 10-4wall_r_linpot   = 1wall_atomtype   = ca  cawall_density    = 
60  60wall_ewald_zfac = 3ewald-geometry  = 3dc

Thanks,Ganj

-- 
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] mdrun error

2018-05-21 Thread Justin Lemkul




On 5/21/18 5:42 PM, rose rahmani wrote:

!!!
I have sheet(at z=0) and 2wall(are close to each other and one of them
begins at z=3.5 and the other at z=~3.8) structures which the other
molecules(water, AA, NA, CL) are BETWEEN sheet and wall structures. before
solvation, i add box size without considering the wall in coordination
because i didn't want that sol molecules enter the space between two carbon
WALLs. After solvation in EM step because of PBC issues i had to increase
the box size in x dimension for 0.094 nm. The box size in z dimension is
almost 3times bigger than the distance between walls and sheet ( box
size=12 nm) because of PBC.

I try to figure out what happens and please correct me if i am wrong;
1, as i can see in .gro file 3 water molecules are in vaccum space so may
feel larger force.

2, some water molecules are between to carbon walls(maybe they could get
there because of 0.094nm space that i added to x dimension)

3, number of water molecules is not enough for this size of system.

4, i know that the system in energy minimization (before pulling) minimized
with minus Kj/mol and didn't fluctuate, but GROMACS said in didn't get
converged.

5, i constraint hbonds and because of that i decided to choose dt=2fs. As
far as i know hbonds have the highest vibrational frequency and least
time so i choose 2fs...

Could you please help me which one caused to problem?


It could be any number of things, perhaps even things not listed here. 
Be a scientist - change one thing at a time until you uncover the source 
of the problem. As it stands, your system has far too many variables to 
assign blame to any one of them.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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] mdrun error

2018-05-21 Thread rose rahmani

!!!
I have sheet(at z=0) and 2wall(are close to each other and one of them
begins at z=3.5 and the other at z=~3.8) structures which the other
molecules(water, AA, NA, CL) are BETWEEN sheet and wall structures. before
solvation, i add box size without considering the wall in coordination
because i didn't want that sol molecules enter the space between two carbon
WALLs. After solvation in EM step because of PBC issues i had to increase
the box size in x dimension for 0.094 nm. The box size in z dimension is
almost 3times bigger than the distance between walls and sheet ( box
size=12 nm) because of PBC.

I try to figure out what happens and please correct me if i am wrong;
1, as i can see in .gro file 3 water molecules are in vaccum space so may
feel larger force.

2, some water molecules are between to carbon walls(maybe they could get
there because of 0.094nm space that i added to x dimension)

3, number of water molecules is not enough for this size of system.

4, i know that the system in energy minimization (before pulling) minimized
with minus Kj/mol and didn't fluctuate, but GROMACS said in didn't get
converged.

5, i constraint hbonds and because of that i decided to choose dt=2fs. As
far as i know hbonds have the highest vibrational frequency and least
time so i choose 2fs...

Could you please help me which one caused to problem?

Regards
-Rose

On Tue, 22 May 2018, 01:19 Justin Lemkul,  wrote:

>
>
> On 5/21/18 4:47 PM, rose rahmani wrote:
> > Hi,
> >
> > I do umbrella sampling with GROMACS4.5.4 version. I got this error
> > "A charge group moved too far between two domain decomposition steps."
> > But when i try it in another computer(version 4.5.4 was also installed
> > there) this error doesn't exist any more! How could it be possible?which
> > one is correct?
>
> Welcome to the stochastic nature of MD. You have an unstable system that
> occasionally works. Don't trust it - figure out where the instability
> comes from and/or prepare the system more gently.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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] mdrun error

2018-05-21 Thread Justin Lemkul




On 5/21/18 4:47 PM, rose rahmani wrote:

Hi,

I do umbrella sampling with GROMACS4.5.4 version. I got this error
"A charge group moved too far between two domain decomposition steps."
But when i try it in another computer(version 4.5.4 was also installed
there) this error doesn't exist any more! How could it be possible?which
one is correct?


Welcome to the stochastic nature of MD. You have an unstable system that 
occasionally works. Don't trust it - figure out where the instability 
comes from and/or prepare the system more gently.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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] mdrun error

2018-05-21 Thread rose rahmani

Hi,

I do umbrella sampling with GROMACS4.5.4 version. I got this error
"A charge group moved too far between two domain decomposition steps."
But when i try it in another computer(version 4.5.4 was also installed
there) this error doesn't exist any more! How could it be possible?which
one is correct?

Best
-- 
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] mdrun error

2017-03-29 Thread Justin Lemkul




On 3/29/17 11:49 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello,
After equilibrating my system for 100 ns( during which there was restraint
on the protein letting the lipids to equilibrate), when I am trying to run
my unrestrained run I am getting the following errors:
1. "bonds that rotated more than 30 degree"
2. "1 particles communicated to PME rank 0 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x"
3. "Listed nonbonded interaction between particles 71916 and 71920
at distance 5.535 which is larger than the table limit 2.215 nm."

What might be the reason for this error. I thought 100ns is enough for
equilibration.



Something is likely topologically unsound.  The restraints were probably masking 
an underlying issue (100 ns is way longer than one normally runs for restrained 
dynamics, FWIW).


-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

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

[gmx-users] mdrun error

2017-03-29 Thread amitbehra

Hello,
After equilibrating my system for 100 ns( during which there was restraint
on the protein letting the lipids to equilibrate), when I am trying to run
my unrestrained run I am getting the following errors:
1. "bonds that rotated more than 30 degree"
2. "1 particles communicated to PME rank 0 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x"
3. "Listed nonbonded interaction between particles 71916 and 71920
at distance 5.535 which is larger than the table limit 2.215 nm."

What might be the reason for this error. I thought 100ns is enough for
equilibration.

Thanks,
Amit Behera
Research Scholar,
IISc.

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-- 
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] mdrun error

2016-06-12 Thread Mark Abraham

Hi,

Is your box changing shape? You've switched from isotropic to anisotropic,
and to a thermostat that is not tolerant of changes to the size/shape of
the box. Change one thing at a time.

Mark

On Sun, Jun 12, 2016 at 8:09 PM mahdiyeh poorsargol <
poorsargol@gmail.com> wrote:

> Dear gmx users,
> I am using gromacs 4.6.5 to simulate a system including: graphene + water +
> surfactant. I used the box with size 7.4,7.4,9.4 (nm3) and a cutoff
> distance of 1.2 nm. I have done nvt with Berendsen thermostat for 1 ns ,
> npt with Berendsen thermostat and Berendsen barostat for 2 ns (pcoupltype=
> isotropic). when I mdrun with Nose-hoover thermostat and Parrinello-Rahman
> barostat for 40 ns (pcoupltype= anisotropic), it gave me the following
> error:
>
>
> Fatal error:
> Step 109048: The X-size (0.679861) times the triclinic skew factor
> (1.00) is smaller than the smallest allowed cell size (0.679862) for
> domain decomposition grid cell 4 0 1
>
> I would be pleased if anyone could help me how to fix this.
> mahdiyeh
> --
> 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] mdrun error

2016-06-12 Thread mahdiyeh poorsargol

Dear gmx users,
I am using gromacs 4.6.5 to simulate a system including: graphene + water +
surfactant. I used the box with size 7.4,7.4,9.4 (nm3) and a cutoff
distance of 1.2 nm. I have done nvt with Berendsen thermostat for 1 ns ,
npt with Berendsen thermostat and Berendsen barostat for 2 ns (pcoupltype=
isotropic). when I mdrun with Nose-hoover thermostat and Parrinello-Rahman
barostat for 40 ns (pcoupltype= anisotropic), it gave me the following
error:


Fatal error:
Step 109048: The X-size (0.679861) times the triclinic skew factor
(1.00) is smaller than the smallest allowed cell size (0.679862) for
domain decomposition grid cell 4 0 1

I would be pleased if anyone could help me how to fix this.
mahdiyeh
-- 
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] mdrun error

2015-12-21 Thread محمد گره گشا

Dears all
Hi
we run a MD simulation. but when we using mdrun command to energy
minimization encountered this message: "killed" and No error appears.
so anyone can help please?
thank you

On Mon, Dec 21, 2015 at 10:08 AM, محمد گره گشا 
wrote:

> Hi all dears
>  We run a MD simulation. and when we use mdrun command to energy
> minimization face this message: 'Killed' and no error.
> anyone can help we please?
> thanks
>
-- 
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] mdrun error

2015-12-21 Thread محمد گره گشا

Dear all

I am a beginner in MD simulation using OPLSA force field in Gromacs . I
prepared ligand-protein complex step by step:
1- I build topology and gro file of protein
2- Add itp and gro file of ligand to it. I build them by
http://erg.biophys.msu.ru/tpp/ and  PRDRUG , respectively.( I don't know,
my gro file is correct or not because I buld it PRDRUG.)
3- Partial charge atoms of ligand were calculated using Goussian.
In this step, there is an error: the sum of the two largest charge group
radii is larger than rlist-rvdw/rcoulomb

Would you please help have can I solve it?
I add itp and partial charge to this message.

; LIG - topology generator
; created by Erg Research Group
; MSU, Biology Faculty, Department of Biophysics
; --
; Topology was prepared for use with the forcefield: 

[ moleculetype ]
  LIG 3

; Force constant parameters
#define dfLIG_bon_1 1 0.140  3.92e+05 ;1
#define dfLIG_bon_3 1 0.136  3.77e+05 ;1
#define dfLIG_bon_5 1 0.136  3.77e+05 ;1
#define dfLIG_bon_7 1 0.108  3.07e+05 ;1
#define dfLIG_bon_9 1 0.140  3.92e+05 ;1
#define dfLIG_bon_151 0.134  4.04e+05 ;1
#define dfLIG_bon_171 0.134  4.04e+05 ;1
#define dfLIG_bon_181 0.151  2.65e+05 ;1
#define dfLIG_bon_201 0.109  2.85e+05 ;1
#define dfLIG_bon_331 0.141  2.68e+05 ;1
#define dfLIG_ang_1 1 120.0  527.2 ;2
#define dfLIG_ang_2 1 120.0  585.8 ;2
#define dfLIG_ang_8 1 120.0  292.9 ;2
#define dfLIG_ang_221 124.0  585.8 ;2
#define dfLIG_ang_241 116.0  292.9 ;2
#define dfLIG_ang_271 116.0  585.8 ;2
#define dfLIG_ang_281 117.0  585.8 ;2
#define dfLIG_ang_291 109.5  334.7 ;2
#define dfLIG_ang_301 109.5  292.9 ;2
#define dfLIG_ang_341 107.8  276.1 ;2
#define dfLIG_ang_531 111.0  627.6 ;2
#define dfLIG_dih_1 3 +30.3  +0.0 -30.3  +0.0  +0.0  +0.0 ;3
#define dfLIG_dih_9 3 +12.6  +0.0 -12.6  +0.0  +0.0  +0.0 ;3
#define dfLIG_dih_163 +12.6  +0.0 -12.6  +0.0  +0.0  +0.0 ;3
#define dfLIG_dih_453  +0.0  +0.0  +0.0  +0.0  +0.0  +0.0 ;3
#define dfLIG_dih_853  +1.6  +4.8  +0.0  -6.4  +0.0  +0.0 ;3

[ atoms ]
  1  opls_199   1  LIG   CAA  1  0.179016  12.011000 ;  C(O,Me): anisole
  2  opls_199   1  LIG   CAB  2  0.076137  12.011000 ;  C(O,Me): anisole
  3  opls_145   1  LIG   CAC  3 -0.190807  12.011000 ;  Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
  4  opls_523   1  LIG   CAD  4  0.066027  12.011000 ;  C3  in pyridine
for
  5  opls_522   1  LIG   CAE  5 -0.114338  12.011000 ;  C2  in pyridine
charges
  6  opls_145   1  LIG   CAF  6 -0.161633  12.011000 ;  Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
  7  opls_522   1  LIG   CAI  7  0.235355  12.011000 ;  C2  in pyridine
charges
  8  opls_521   1  LIG   CAG  8 -0.255026  12.011000 ;  C1  in pyridine
CHELPG
  9  opls_521   1  LIG   CAH  9  0.040392  12.011000 ;  C1  in pyridine
CHELPG
 10  opls_520   1  LIG   NAJ 10 -0.352241  14.006700 ;  N   in pyridine
6-31G*
 11  opls_136   1  LIG   CAK 11 -0.312125  12.011000 ;  alkane CH2
 12  opls_145   1  LIG   CAL 12  0.097277  12.011000 ;  Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
 13  opls_145   1  LIG   CAM 13 -0.280318  12.011000 ;  Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
 14  opls_199   1  LIG   CAU 14 -0.215985  12.011000 ;  C(O,Me): anisole
 15  opls_199   1  LIG   CAT 15 -0.213602  12.011000 ;  C(O,Me): anisole
 16  opls_145   1  LIG   CAP 16 -0.184387  12.011000 ;  Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
 17  opls_145   1  LIG   CAQ 17 -0.224424  12.011000 ;  Benzene C - 12
site JACS,112,4768-90. Use #145B for biphenyl
 18  opls_179   1  LIG   OAV 18 -0.342419  15.999400 ;  O: anisole
 19  opls_179   1  LIG   OAW 19 -0.333900  15.999400 ;  O: anisole
 20  opls_181   1  LIG   CAX 20 -0.212853  12.011000 ;  C(H3OR): methyl
ether
 21  opls_181   1  LIG   CAY 21 -0.228460  12.011000 ;  C(H3OR): methyl
ether
 22  opls_179   1  LIG   OAS 22 -0.355106  15.999400 ;  O: anisole
 23  opls_179   1  LIG   OAR 23 -0.367769  15.999400 ;  O: anisole
 24  opls_181   1  LIG   CAO 24  0.206705  12.011000 ;  C(H3OR): methyl
ether
 25  opls_181   1  LIG   CAN 25  0.183982  12.011000 ;  C(H3OR): methyl
ether
 26  opls_146   1  LIG   HAC  3  0.175586  1.008000 ;  Benzene H - 12
site.
 27  opls_146   1  LIG   HAF  6  0.158419  1.008000 ;  Benzene H - 12
site.
 28  opls_525   1  LIG   HAH  7  0.158955  1.008000 ;  H2  in pyridine
 29  opls_524   1  LIG   HAG  8  0.166532  1.008000 ;  H1  in pyridine
520-619
 30  opls_140   1  LIG   HAK 11  0.168958  1.008000 ;  alkane H.
 31  opls_140   1  LIG   HAL 11  0.156734  1.008000 ;  alkane H.
 32  opls_146   1  LIG   HAM 13  0.170382  1.008000 ;  Benzene H - 12
site.
 33  opls_146   1  LIG   HAP 16  0.152440  1.008000 ;  Benzene H - 12
site.
 34  opls_146   1  LIG

[gmx-users] mdrun error

2015-12-20 Thread محمد گره گشا

Hi all dears
 We run a MD simulation. and when we use mdrun command to energy
minimization face this message: 'Killed' and no error.
anyone can help we please?
thanks
-- 
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] mdrun error

2015-11-26 Thread Elton Carvalho

Dear Golnaz,

Depending on how your system is set up, you have a few options, listed
here in the order I would try them (knowing no details about your
system):

1) If you have less than, say, 100~500 atoms per CPU core (depending
on your network), use less nodes to run the simulation. The
parallellism starts getting worse at this point:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Approaching_the_scaling_limit

2) If your box is high enough on the z direction, try mdrun -dd 1 1 4
(with 4 here being the number of nodes you're running on. Take into
account step 1 above), so that you don't have to do DD in the short
dimensions.

3) Enlarge your box if it physically makes sense: What's the
surfactant concentration you're aiming for? Note you'll have to
replicate rour graphene sheet so it fills up your box without strain.
gmx genconf -nbox 2 2 1 may help you. Note you'll have to redo the
topology.

Cheers,

On Thu, Nov 26, 2015 at 11:11 AM, Golnaz Roudsari  wrote:
> Dear users
> I got this error in my mdrun There is no domain decomposition for 4 nodes
> that are compatible with the given box and a minimum cell size of 7.1147
> nm. my system contains graphene and surfactants. In last box I put graphene
> in the middle of my box and the graphene was npbc and the mdrun went well,
> then I put a pbc graphene and the x and y dimension box fixed to match the
> size of graphene sheet. but in energy minimization step. I get this error!
> Can I put the x, y dimension of my box larger than pbc graphene?
> thank you for any suggestion
> Golnaz
> --
> 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.

-- 
Elton Carvalho
-- 
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] mdrun error

2015-11-26 Thread Golnaz Roudsari

Dear users
I got this error in my mdrun There is no domain decomposition for 4 nodes
that are compatible with the given box and a minimum cell size of 7.1147
nm. my system contains graphene and surfactants. In last box I put graphene
in the middle of my box and the graphene was npbc and the mdrun went well,
then I put a pbc graphene and the x and y dimension box fixed to match the
size of graphene sheet. but in energy minimization step. I get this error!
Can I put the x, y dimension of my box larger than pbc graphene?
thank you for any suggestion
Golnaz
-- 
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] mdrun error

2015-08-31 Thread Justin Lemkul




On 8/31/15 12:41 AM, tasneem kausar wrote:

  Hi,
I am trying to run final MD.
The job terminated with the following error message.

Fatal error:
The initial cell size (0.875477) is smaller than the cell size limit
(0.876000), change options -dd, -rdd or -rcon, see the log file for details


What is the problem with the system?



Your system's dimensions are changing rapidly, which causes a DD failure. Be 
sure there's nothing physically wrong before trying to circumvent the issue. 
Usually a large expansion or collapse of DD cells indicates physical instability.


-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

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

Re: [gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box

2015-05-06 Thread Justin Lemkul




On 5/6/15 7:26 AM, Mark Abraham wrote:

On Wed, May 6, 2015 at 9:01 AM Seyed Mojtaba Rezaei Sani 
s.m.rezaeis...@gmail.com wrote:


Dear Justin

Thanks for your kind response. I didn't notice the point you mentioned. It
seems that grompp doesn't care the difference betwen vdwq and vdw-q.
however, I corrected the script. The error remains even in the case of
choosing 2 nodes. The only way to have a successful run is a serial
calculation.



Then that's life (except that if your protein is non-spheroidal, you might
have better luck with the long axis aligned to the z-axis).

The domain decomposition code expects bonded interactions to be of shorter
range than short-ranged non-bonded interactions, so will not produce a
decomposition that has a bonded interaction that starts in one domain,
crosses another domain, leaves by the opposite face, and reaches a third
domain. This is implemented by setting a minimum size for domains based on
many properties of the observed starting structure. There's a brief summary
of these choices printed in every .log file.

The use of couple-intramol triggers the generation of atypical
interactions, that are implemented like bonds as far as the DD code knows,
and for a protein those bonds are so much longer that they set a minimum
size that means a decomposition is infeasible.

AFAIK, FEP on a whole protein isn't going to work at all anyway.



True.  But is DOX isn't a protein; it's doxorubicin.  There is no reason that 
I can think of that would cause DD to fail unless the box is unreasonably small. 
 An extension of normal interactions out to 1.9 nm should be within normal 
limits if the box is of adequate size.  Perhaps the OP can give us more 
information (linking the .log rather than trying to attach it) and describing 
the box size.


-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

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

Re: [gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box

2015-05-06 Thread Seyed Mojtaba Rezaei Sani

Thank you Mark. As Justin suggested I increased the box size and now I can
run the job on 4 machines. The old md.log file can be found here:

https://www.dropbox.com/s/bbmqln6oqjyus0b/md.log?dl=0

My first choice for the box was a dodecahedron one with the option -d 1nm
which now is increased to 2 nm.
Thank you Justin for your useful help.

On Wed, May 6, 2015 at 4:10 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/6/15 7:26 AM, Mark Abraham wrote:

 On Wed, May 6, 2015 at 9:01 AM Seyed Mojtaba Rezaei Sani 
 s.m.rezaeis...@gmail.com wrote:

  Dear Justin

 Thanks for your kind response. I didn't notice the point you mentioned.
 It
 seems that grompp doesn't care the difference betwen vdwq and vdw-q.
 however, I corrected the script. The error remains even in the case of
 choosing 2 nodes. The only way to have a successful run is a serial
 calculation.



 Then that's life (except that if your protein is non-spheroidal, you might
 have better luck with the long axis aligned to the z-axis).

 The domain decomposition code expects bonded interactions to be of shorter
 range than short-ranged non-bonded interactions, so will not produce a
 decomposition that has a bonded interaction that starts in one domain,
 crosses another domain, leaves by the opposite face, and reaches a third
 domain. This is implemented by setting a minimum size for domains based on
 many properties of the observed starting structure. There's a brief
 summary
 of these choices printed in every .log file.

 The use of couple-intramol triggers the generation of atypical
 interactions, that are implemented like bonds as far as the DD code knows,
 and for a protein those bonds are so much longer that they set a minimum
 size that means a decomposition is infeasible.

 AFAIK, FEP on a whole protein isn't going to work at all anyway.


 True.  But is DOX isn't a protein; it's doxorubicin.  There is no reason
 that I can think of that would cause DD to fail unless the box is
 unreasonably small.  An extension of normal interactions out to 1.9 nm
 should be within normal limits if the box is of adequate size.  Perhaps the
 OP can give us more information (linking the .log rather than trying to
 attach it) and describing the box size.


 -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

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




-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)
-- 
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] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box

2015-05-05 Thread Seyed Mojtaba Rezaei Sani

Dear gmx users,

Perhaps my problem is a repetitive question in the forum but I couldn't
find a trouble-shooter response for my case.
I am running a stochastic dynamics calculation for a solution of
doxorubicin. The following error occurs while the calculation runs:

Fatal error:
There is no domain decomposition for x nodes that is compatible with the
given box and a minimum cell size of 1.9433 nm
Change the number of nodes or mdrun option -rdd or -dds

I have tried several numbers of nodes resulting in the same error. Here is
the mdp file:

integrator   = sd
nsteps   = 100
dt   = 0.002
nstenergy= 1000
nstlog   = 5000
; turn off trajectory writing
nstxout  = 0
nstvout  = 0
; cut-offs at 1nm
rlist= 1.0
nstlist  = 10
coulombtype  = pme
vdw-type = cut-off
rvdw = 1.0
constraints  = all-bonds
; set temperature to 300K
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.2
ref-t= 300
; and pressure to 1 bar
pcoupl   = parrinello-rahman
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
; and set the free energy parameters
free-energy  = yes
couple-moltype   = DOX
init-lambda  = 0
; these 'soft-core' parameters make sure we never get overlapping
; charges as lambda goes to 0
sc-power = 1
sc-sigma = 0.3
sc-alpha = 1.0
; we still want the molecule to interact with itself at lambda=0
couple-intramol  = no
couple-lambda1   = vdwq
couple-lambda0   = none
foreign-lambda   = 0 0.2 0.4 0.6 0.8 0.9 1


would you give me some hints?
Thanks in advance.

-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)
-- 
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] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box

2015-05-05 Thread Justin Lemkul




On 5/5/15 8:48 AM, Seyed Mojtaba Rezaei Sani wrote:

Dear gmx users,

Perhaps my problem is a repetitive question in the forum but I couldn't
find a trouble-shooter response for my case.
I am running a stochastic dynamics calculation for a solution of
doxorubicin. The following error occurs while the calculation runs:

Fatal error:
There is no domain decomposition for x nodes that is compatible with the
given box and a minimum cell size of 1.9433 nm
Change the number of nodes or mdrun option -rdd or -dds

I have tried several numbers of nodes resulting in the same error. Here is
the mdp file:

integrator   = sd
nsteps   = 100
dt   = 0.002
nstenergy= 1000
nstlog   = 5000
; turn off trajectory writing
nstxout  = 0
nstvout  = 0
; cut-offs at 1nm
rlist= 1.0
nstlist  = 10
coulombtype  = pme
vdw-type = cut-off
rvdw = 1.0
constraints  = all-bonds
; set temperature to 300K
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.2
ref-t= 300
; and pressure to 1 bar
pcoupl   = parrinello-rahman
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
; and set the free energy parameters
free-energy  = yes
couple-moltype   = DOX
init-lambda  = 0
; these 'soft-core' parameters make sure we never get overlapping
; charges as lambda goes to 0
sc-power = 1
sc-sigma = 0.3
sc-alpha = 1.0
; we still want the molecule to interact with itself at lambda=0
couple-intramol  = no


This is what triggers the error.  Note from the manual, for couple-intramol = 
no:

All intra-molecular non-bonded interactions for moleculetype couple-moltype are 
replaced by exclusions and explicit pair interactions. In this manner the 
decoupled state of the molecule corresponds to the proper vacuum state without 
periodicity effects.


The added exclusions and pairs require larger DD cells to be constructed because 
these bonded interactions occur over larger distances than normal.  This limits 
the size of the DD cells and hence how many processors/cores you can use.  You 
haven't said how many you're trying to use, but the solution is simply to use fewer.



couple-lambda1   = vdwq


The option is vdw-q but I don't know if grompp magically translates it.  Just 
check.


-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

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

Re: [gmx-users] mdrun error message in Computing Cluster

2014-10-31 Thread Mark Abraham

Hi,

I've never seen that error. I hope you have a compelling scientific reason
for installing such a slow old version :-)

Mark
On Oct 31, 2014 1:58 AM, Agnivo Gosai agnivogromac...@gmail.com wrote:

 Dear Users

 I compiled double precision Gromacs 4.5.6 in my university cluster ( named
 CyEnce ).
 It is the serial version as I did not compile mdrun separately as parallel
 mdrun.
 I followed the procedure in the below mentioned link :-
 http://ringo.ams.sunysb.edu/index.php/Compiling_GROMACS_on_Cluster
 But while using mdrun I am getting the following error :-

 Reading file em.tpr, VERSION 4.5.6 (double precision)
 Starting 16 threads
 tMPI Fatal error in pthreads.c, line 202: Failed to create POSIX
 thread:Resource temporarily unavailable, rc=11
 Aborted

 I am not sure as to what this means. Any suggestions please ??

 Thanks  Regards
 Agnivo Gosai
 Grad Student, Iowa State University.
 --
 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] mdrun error message in Computing Cluster

2014-10-30 Thread Agnivo Gosai

Dear Users

I compiled double precision Gromacs 4.5.6 in my university cluster ( named
CyEnce ).
It is the serial version as I did not compile mdrun separately as parallel
mdrun.
I followed the procedure in the below mentioned link :-
http://ringo.ams.sunysb.edu/index.php/Compiling_GROMACS_on_Cluster
But while using mdrun I am getting the following error :-

Reading file em.tpr, VERSION 4.5.6 (double precision)
Starting 16 threads
tMPI Fatal error in pthreads.c, line 202: Failed to create POSIX
thread:Resource temporarily unavailable, rc=11
Aborted

I am not sure as to what this means. Any suggestions please ??

Thanks  Regards
Agnivo Gosai
Grad Student, Iowa State University.
-- 
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] mdrun error

2014-08-25 Thread Lovika Moudgil

I am  trying to have a system of  GNPs with aminoacid and stabilizer i.e
Sodium Citrate ...and this hydrogen is of Sodium Citrate .  moving
molecule is not working for me!!!

Regards
Lovika


On Mon, Aug 25, 2014 at 10:52 AM, Kester Wong kester2...@ibs.re.kr wrote:

 If the H-atom is constituent of a molecule (e.g. H2O), then you could also
 try moving the molecule coordinates and see how it goes.

 I had a similar issue, but moving the molecule by an angstrom worked in my
 case. Good luck!



 Regards,

 Kester



 - 원본 메일 -

 *보낸사람* : Lovika Moudgil lovikamoud...@gmail.com
 *받는사람* : gmx-us...@gromacs.org
 *받은날짜* : 2014년 8월 25일(월) 13:52:49
 *제목* : Re: [gmx-users] mdrun error

 Thanks for reply Justin and Kester...Ya my geometry is getting distorted
 and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the
 error is same


 Regards
 Lovika


 On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong  wrote:

  Dear Lovika,
 
 
  Have you looked into atom 19 specifically? Perhaps, changing the
  coordinate of atom 19  manually, and let it do another minimisation run
  would solve the issue?
 
 
 
  Regards,
 
  Kester
 
 
  - 원본 메일 -
 
  *보낸사람* : Lovika Moudgil
  *받는사람* :
  *받은날짜* : 2014년 8월 24일(일) 18:28:06
  *제목* : [gmx-users] mdrun error
 
  Hi everyone ,
 
  Need some help .I have got an error in my mdrun . Upto grompp every thing
  was fine but when I give command for mdrun ,It stops with this ...
  Steepest Descents:
 Tolerance (Fmax)   =  1.0e+03
 Number of steps=1
  Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax= inf, atom= 19
  Energy minimization has stopped, but the forces have not converged to the
  requested precision Fmax  1000 (which may not be possible for your system).
  It stopped because the algorithm tried to make a new step whose size was too
  small, or there was no change in the energy since last step. Either way, we
  regard the minimization as converged to within the available machine
  precision, given your starting configuration and EM parameters.
 
  Double precision normally gives you higher accuracy, but this is often not
  needed for preparing to run molecular dynamics.
  You might need to increase your constraint accuracy, or turn
  off constraints altogether (set constraints = none in mdp file)
 
  writing lowest energy coordinates.
 
 
  Steepest Descents converged to machine precision in 15 steps,
  but did not reach the requested Fmax  1000.
  Potential Energy  =  2.0853354e+18
  Maximum force =inf on atom 19
  Norm of force =  1.7429674e+18
 
  constraints are all ready none ...Please help me what should I do to solve
  this .
  Thanks and Regards
  Lovika
  --
  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 
  visithttps://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.
 
 
 --
 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 
 visithttps://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.


-- 
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] mdrun error

2014-08-25 Thread Mark Abraham

Hi,

Use a visualization program and see what you learn...

Mark


On Mon, Aug 25, 2014 at 8:26 AM, Lovika Moudgil lovikamoud...@gmail.com
wrote:

 I am  trying to have a system of  GNPs with aminoacid and stabilizer i.e
 Sodium Citrate ...and this hydrogen is of Sodium Citrate .  moving
 molecule is not working for me!!!

 Regards
 Lovika


 On Mon, Aug 25, 2014 at 10:52 AM, Kester Wong kester2...@ibs.re.kr
 wrote:

  If the H-atom is constituent of a molecule (e.g. H2O), then you could
 also
  try moving the molecule coordinates and see how it goes.
 
  I had a similar issue, but moving the molecule by an angstrom worked in
 my
  case. Good luck!
 
 
 
  Regards,
 
  Kester
 
 
 
  - 원본 메일 -
 
  *보낸사람* : Lovika Moudgil lovikamoud...@gmail.com
  *받는사람* : gmx-us...@gromacs.org
  *받은날짜* : 2014년 8월 25일(월) 13:52:49
  *제목* : Re: [gmx-users] mdrun error
 
  Thanks for reply Justin and Kester...Ya my geometry is getting distorted
  and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the
  error is same
 
 
  Regards
  Lovika
 
 
  On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong  wrote:
 
   Dear Lovika,
  
  
   Have you looked into atom 19 specifically? Perhaps, changing the
   coordinate of atom 19  manually, and let it do another minimisation run
   would solve the issue?
  
  
  
   Regards,
  
   Kester
  
  
   - 원본 메일 -
  
   *보낸사람* : Lovika Moudgil
   *받는사람* :
   *받은날짜* : 2014년 8월 24일(일) 18:28:06
   *제목* : [gmx-users] mdrun error
  
   Hi everyone ,
  
   Need some help .I have got an error in my mdrun . Upto grompp every
 thing
   was fine but when I give command for mdrun ,It stops with this ...
   Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps=1
   Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax= inf,
 atom= 19
   Energy minimization has stopped, but the forces have not converged to
 the
   requested precision Fmax  1000 (which may not be possible for your
 system).
   It stopped because the algorithm tried to make a new step whose size
 was too
   small, or there was no change in the energy since last step. Either
 way, we
   regard the minimization as converged to within the available machine
   precision, given your starting configuration and EM parameters.
  
   Double precision normally gives you higher accuracy, but this is often
 not
   needed for preparing to run molecular dynamics.
   You might need to increase your constraint accuracy, or turn
   off constraints altogether (set constraints = none in mdp file)
  
   writing lowest energy coordinates.
  
  
   Steepest Descents converged to machine precision in 15 steps,
   but did not reach the requested Fmax  1000.
   Potential Energy  =  2.0853354e+18
   Maximum force =inf on atom 19
   Norm of force =  1.7429674e+18
  
   constraints are all ready none ...Please help me what should I do to
 solve
   this .
   Thanks and Regards
   Lovika
   --
   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 visithttps://
 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.
  
  
  --
  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 visithttps://
 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.
 
 
 --
 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

[gmx-users] mdrun error

2014-08-24 Thread Lovika Moudgil

Hi everyone ,

Need some help .I have got an error in my mdrun . Upto grompp every thing
was fine but when I give command for mdrun ,It stops with this ...
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=1
Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax= inf, atom= 19
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax  1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.


Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1000.
Potential Energy  =  2.0853354e+18
Maximum force =inf on atom 19
Norm of force =  1.7429674e+18

constraints are all ready none ...Please help me what should I do to solve
this .
Thanks and Regards
Lovika
-- 
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] mdrun error

2014-08-24 Thread Justin Lemkul




On 8/24/14, 5:28 AM, Lovika Moudgil wrote:

Hi everyone ,

Need some help .I have got an error in my mdrun . Upto grompp every thing
was fine but when I give command for mdrun ,It stops with this ...
Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=1
Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax= inf, atom= 19
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax  1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.


Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1000.
Potential Energy  =  2.0853354e+18
Maximum force =inf on atom 19
Norm of force =  1.7429674e+18

constraints are all ready none ...Please help me what should I do to solve
this .


You have an infinite force, so that means severe atomic clashes or a totally 
distorted geometry.  mdrun tells you atom 19 is in the neighborhood of the 
problem, so visualize and see.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

Dear Lovika,Have you looked into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue?Regards,Kester- 원본 메일 -보낸사람 : Lovika Moudgil lovikamoud...@gmail.com받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 24일(일) 18:28:06제목 : [gmx-users] mdrun errorHi everyone ,

Need some help .I have got an error in my mdrun . Upto grompp every thing
was fine but when I give command for mdrun ,It stops with this ...
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps=1
Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, atom= 19
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax 1000.
Potential Energy = 2.0853354e+18
Maximum force =inf on atom 19
Norm of force = 1.7429674e+18

constraints are all ready none ...Please help me what should I do to solve
this .
Thanks and Regards
Lovika
--
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] mdrun error

2014-08-24 Thread Lovika Moudgil

Thanks for reply Justin and Kester...Ya my geometry is getting distorted
and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the
error is same


Regards
Lovika


On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong kester2...@ibs.re.kr wrote:

 Dear Lovika,


 Have you looked into atom 19 specifically? Perhaps, changing the
 coordinate of atom 19  manually, and let it do another minimisation run
 would solve the issue?



 Regards,

 Kester


 - 원본 메일 -

 *보낸사람* : Lovika Moudgil lovikamoud...@gmail.com
 *받는사람* : gmx-us...@gromacs.org
 *받은날짜* : 2014년 8월 24일(일) 18:28:06
 *제목* : [gmx-users] mdrun error

 Hi everyone ,

 Need some help .I have got an error in my mdrun . Upto grompp every thing
 was fine but when I give command for mdrun ,It stops with this ...
 Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=1
 Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax= inf, atom= 19
 Energy minimization has stopped, but the forces have not converged to the
 requested precision Fmax  1000 (which may not be possible for your system).
 It stopped because the algorithm tried to make a new step whose size was too
 small, or there was no change in the energy since last step. Either way, we
 regard the minimization as converged to within the available machine
 precision, given your starting configuration and EM parameters.

 Double precision normally gives you higher accuracy, but this is often not
 needed for preparing to run molecular dynamics.
 You might need to increase your constraint accuracy, or turn
 off constraints altogether (set constraints = none in mdp file)

 writing lowest energy coordinates.


 Steepest Descents converged to machine precision in 15 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  =  2.0853354e+18
 Maximum force =inf on atom 19
 Norm of force =  1.7429674e+18

 constraints are all ready none ...Please help me what should I do to solve
 this .
 Thanks and Regards
 Lovika
 --
 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 
 visithttps://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.


-- 
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] mdrun error

2014-08-24 Thread Kester Wong

If the H-atom is constituent of a molecule (e.g. H2O), then you could also try moving the molecule coordinates and see how it goes.I had a similar issue, but moving the molecule by an angstrom worked in my case. Good luck!Regards,Kester- 원본 메일 -보낸사람 : Lovika Moudgil lovikamoud...@gmail.com받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 25일(월) 13:52:49제목 : Re: [gmx-users] mdrun errorThanks for reply Justin and Kester...Ya my geometry is getting distorted
and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the
error is same

Regards
Lovika

On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong <kester2...@ibs.re.kr> wrote:

Dear Lovika,

Have you looked into atom 19 specifically? Perhaps, changing the
coordinate of atom 19 manually, and let it do another minimisation run
would solve the issue?

Regards,

Kester

- 원본 메일 -

*보낸사람* : Lovika Moudgil <lovikamoud...@gmail.com>
*받는사람* : <gmx-us...@gromacs.org>
*받은날짜* : 2014년 8월 24일(일) 18:28:06
*제목* : [gmx-users] mdrun error

Hi everyone ,

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax 1000.
Potential Energy = 2.0853354e+18
Maximum force =inf on atom 19
Norm of force = 1.7429674e+18

constraints are all ready none ...Please help me what should I do to solve
this .
Thanks and Regards
Lovika
--
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 visithttps://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.

--
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] mdrun error messages

2014-07-15 Thread Andy Chao

Dear GROMACS Users:

As I mentioned, I got the following log file when I used the mdrun
command.  I installed GROMACS on my virtual machine.  Is there any solution
to this problem?

Thanks!

Andy

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  


Changing rlist from 1.05 to 1 for non-bonded 4x4 atom kernels

Input Parameters:
   integrator   = steep
   nsteps   = 200
   init-step= 0
   cutoff-scheme= Verlet
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 100
   comm-mode= Linear
   nstlog   = 1000
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstcalcenergy= 100
   nstenergy= 1000
   nstxtcout= 0
   init-t   = 0
   delta-t  = 0.001
   xtcprec  = 1000
   fourierspacing   = 0.12
   nkx  = 48
   nky  = 48
   nkz  = 48
   pme-order= 4
   ewald-rtol   = 1e-05
   ewald-geometry   = 0
   epsilon-surface  = 0
   optimize-fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = No
   bPrintNHChains   = FALSE
   nsttcouple   = -1
   epc  = No
   epctype  = Isotropic
   nstpcouple   = -1
   tau-p= 1
   ref-p (3x3):
  ref-p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref-p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref-p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord-scaling = No
   posres-com (3):
  posres-com[0]= 0.0e+00
  posres-com[1]= 0.0e+00
  posres-com[2]= 0.0e+00
   posres-comB (3):
  posres-comB[0]= 0.0e+00
  posres-comB[1]= 0.0e+00
  posres-comB[2]= 0.0e+00
   verlet-buffer-drift  = 0.005
   rlist= 1
   rlistlong= 1
   nstcalclr= 10
   rtpi = 0.05
   coulombtype  = PME
   coulomb-modifier = Potential-shift
   rcoulomb-switch  = 0
   rcoulomb = 1
   vdwtype  = Cut-off
   vdw-modifier = Potential-shift
   rvdw-switch  = 0
   rvdw = 1
   epsilon-r= 1
   epsilon-rf   = inf
   tabext   = 1
   implicit-solvent = No
   gb-algorithm = Still
   gb-epsilon-solvent   = 80
   nstgbradii   = 1
   rgbradii = 1
   gb-saltconc  = 0
   gb-obc-alpha = 1
   gb-obc-beta  = 0.8
   gb-obc-gamma = 4.85
   gb-dielectric-offset = 0.009
   sa-algorithm = Ace-approximation
   sa-surface-tension   = 2.05016
   DispCorr = No
   bSimTemp = FALSE
   free-energy  = no
   nwall= 0
   wall-type= 9-3
   wall-atomtype[0] = -1
   wall-atomtype[1] = -1
   wall-density[0]  = 0
   wall-density[1]  = 0
   wall-ewald-zfac  = 3
   pull = no
   rotation = FALSE
   disre= No
   disre-weighting  = Conservative
   disre-mixed  = FALSE
   dr-fc= 1000
   dr-tau   = 0
   nstdisreout  = 100
   orires-fc= 0
   orires-tau   = 0
   nstorireout  = 100
   dihre-fc = 0
   em-stepsize  = 0.01
   em-tol   = 10
   niter= 20
   fc-stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake-tol= 0.0001
   lincs-order  = 4
   lincs-warnangle  = 30
   lincs-iter   = 1
   bd-fric  = 0
   ld-seed  = 1993
   cos-accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   adress   = FALSE
   userint1 = 0
   userint2 = 0
   userint3 = 0
   userint4 = 0
   userreal1= 0
   userreal2= 0
   userreal3= 0
   userreal4= 0
grpopts:
   nrdf:   22677
   ref-t:   0
   tau-t:   0
anneal:  No
ann-npoints:   0
   acc:   0   0   0
   nfreeze:   N

Re: [gmx-users] MDRUN error message

2014-07-10 Thread Justin Lemkul




On 7/10/14, 12:15 AM, Andy Chao wrote:

Dear GROMACS Users:

I used the grompp command to run energy minimization of an ionic liquid
structure according to the following command:

grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr

and then run molecular dynamics simulation as the following:

mdrun -s NPT.tpr -o NPT.trr

when I opend the NPT.trr file, there is nothing inside.  Can you explain
what was wrong?

The last part of the md.log file shows
Initialized non-bonded Ewald correction tables, spacing: 6.26e-04 size: 3836

Pinning threads with an auto-selected logical core stride of 1

Initializing LinNear Constraints Solver



Looks like the run never started.  Do other simulations proceed?

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

Re: [gmx-users] mdrun error messages

2014-07-10 Thread Mark Abraham

That means mdrun exited abnormally, e.g. from some undiscovered bug, or
(more likely) from someone e.g. pressing Ctrl-C on their terminal, or such.

Mark


On Thu, Jul 10, 2014 at 5:46 AM, Andy Chao ac...@energiaq.com wrote:

 Dear GROMACS Users:

 I used the grompp command to run energy minimization of an ionic liquid
 structure according to the following command:

 grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr

 and then run molecular dynamics simulation as the following:

 mdrun -s NPT.tpr -o NPT.trr

 when I opend the NPT.trr file, there is nothing inside.  Can you explain
 what was wrong?

 The last part of the md.log file shows
 Initialized non-bonded Ewald correction tables, spacing: 6.26e-04 size:
 3836

 Pinning threads with an auto-selected logical core stride of 1

 Initializing LinNear Constraints Solver


 Thanks!

 Andy
 --
 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] mdrun error

2014-06-25 Thread Justin Lemkul




On 6/25/14, 8:00 AM, Lovika Moudgil wrote:

Hi Everyone...Need some help...

I got the following error in my mdrun Plese help me to understand this
error...What this error is all about and what should I do to remove this .

---
Program mdrun, VERSION 4.6.5
Source code file:
/home/itlab/Documents/gromacs/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241

Fatal error:
Not enough memory. Failed to realloc 473717812 bytes for grid-index,
grid-index=0x2987d008
(called from file
/home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/nsgrid.c, line 493)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



Your hardware lacks sufficient memory to run the simulation.  Either install 
more memory or find hardware suitable for the simulation.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

Re: [gmx-users] mdrun error

2014-05-20 Thread Lovika Moudgil

Thanks for help Justin.


Regards
Lovika


On Tue, May 20, 2014 at 2:49 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/19/14, 11:24 AM, Lovika Moudgil wrote:

 Hiii Everyone

 I need some helpAs in my grompp command I am getting  warning about
 charge group and rlist 
 Can any body help me to understand this ...

 Warning is
 WARNING 2 [file gro.mdp]:
The sum of the two largest charge group radii (5.930022) is larger than
rlist (1.80)

 and my .mdp file is


 Something is inconsistent; your error message says rlist is 1.8, but your
 .mdp says it is 1.0.

 Regardless, either you have some very nasty charge groups (way too large)
 or you simply have groups broken across PBC, which is not actually a
 problem.  Recent versions of grompp are smart enough to deal with PBC, so
 this would only show up with an old version of Gromacs.

 http://www.gromacs.org/Documentation/Errors#The_sum_
 of_the_two_largest_charge_group_radii_(X)_is_larger_
 than.c2.a0rlist_-_rvdw.2frcoulomb

 -Justin

  ; VARIOUS PREPROCESSING OPTIONS
 ; Preprocessor information: use cpp syntax.
 ; e.g.: -I/home/joe/doe -I/home/mary/roe
 include  =
 ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
 define   =

 ; RUN CONTROL PARAMETERS
 integrator   = md
 ; Start time and timestep in ps
 tinit= 0
 dt   = 0.001
 nsteps   = 0
 ; For exact run continuation or redoing part of a run
 init_step= 0
 ; Part index is updated automatically on checkpointing (keeps files
 separate)
 simulation_part  = 1

 ; number of steps for center of mass motion removal
 nstcomm  = 10

 ; LANGEVIN DYNAMICS OPTIONS
 ; Friction coefficient (amu/ps) and random seed
 bd-fric  = 0
 ld-seed  = 1993

 ; ENERGY MINIMIZATION OPTIONS
 ; Force tolerance and initial step-size
 emtol= 10
 emstep   = 0.01
 ; Max number of iterations in relax_shells
 niter= 20
 ; Step size (ps^2) for minimization of flexible constraints
 fcstep   = 0
 ; Frequency of steepest descents steps when doing CG
 nstcgsteep   = 1000
 nbfgscorr= 10

 ; TEST PARTICLE INSERTION OPTIONS
 rtpi = 0.05

 ; OUTPUT CONTROL OPTIONS
 ; Output frequency for coords (x), velocities (v) and forces (f)
 nstxout  = 100
 nstvout  = 100
 nstfout  = 0
 ; Output frequency for energies to log file and energy file
 nstlog   = 100
 nstcalcenergy= -1
 nstenergy= 100
 ; Output frequency and precision for .xtc file
 nstxtcout= 0
 xtc-precision= 1000
 ; This selects the subset of atoms for the .xtc file. You can
 ; select multiple groups. By default all atoms will be written.
 xtc-grps =
 ; Selection of energy groups
 energygrps   =

 ; NEIGHBORSEARCHING PARAMETERS
 ; nblist update frequency
 nstlist  = 10
 ; ns algorithm (simple or grid)
 ns-type  = Grid
 ; Periodic boundary conditions: xyz, no, xy
 pbc  = xyz
 periodic_molecules   = no
 ; nblist cut-off
 rlist= 1
 ; long-range cut-off for switched potentials
 rlistlong= -1

 ; OPTIONS FOR ELECTROSTATICS AND VDW
 ; Method for doing electrostatics
 coulombtype  = Cut-off
 rcoulomb-switch  = 0
 rcoulomb = 1
 ; Relative dielectric constant for the medium and the reaction field
 epsilon_r= 1
 epsilon_rf   = 1
 ; Method for doing Van der Waals
 vdw-type = Cut-off
 ; cut-off lengths
 rvdw-switch  = 0
 rvdw = 1
 ; Apply long range dispersion corrections for Energy and Pressure
 DispCorr = No
 ; Extension of the potential lookup tables beyond the cut-off
 table-extension  = 1
 ; Seperate tables between energy group pairs
 energygrp_table  =
 ; Spacing for the PME/PPPM FFT grid
 fourierspacing   = 0.12
 ; FFT grid size, when a value is 0 fourierspacing will be used
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 ; EWALD/PME/PPPM parameters
 pme_order= 4
 ewald_rtol   = 1e-05
 ewald_geometry   = 3d
 epsilon_surface  = 0
 optimize_fft = no

 ; IMPLICIT SOLVENT ALGORITHM
 implicit_solvent = No

 ; GENERALIZED BORN ELECTROSTATICS
 ; Algorithm for calculating Born radii
 gb_algorithm = Still
 ; Frequency of calculating the Born radii inside rlist
 nstgbradii   = 1
 ; Cutoff for Born radii calculation; the contribution from atoms
 ; between rlist and rgbradii is updated every nstlist steps
 rgbradii = 1
 ; Dielectric coefficient of

Re: [gmx-users] mdrun error

2014-05-19 Thread Lovika Moudgil

Hiii Everyone

I need some helpAs in my grompp command I am getting  warning about
charge group and rlist 
Can any body help me to understand this ...

Warning is
WARNING 2 [file gro.mdp]:
  The sum of the two largest charge group radii (5.930022) is larger than
  rlist (1.80)

and my .mdp file is

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include  =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 0
; For exact run continuation or redoing part of a run
init_step= 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1

; number of steps for center of mass motion removal
nstcomm  = 10

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 100
nstcalcenergy= -1
nstenergy= 100
; Output frequency and precision for .xtc file
nstxtcout= 0
xtc-precision= 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns-type  = Grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1
; long-range cut-off for switched potentials
rlistlong= -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 80
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension   = -1

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl   = No
nsttcouple   = -1
nh-chain-length  = 10
; Groups to couple separately
tc-grps  =
; Time constant (ps) and reference temperature (K)

Re: [gmx-users] mdrun error

2014-05-19 Thread Justin Lemkul




On 5/19/14, 11:24 AM, Lovika Moudgil wrote:

Hiii Everyone

I need some helpAs in my grompp command I am getting  warning about
charge group and rlist 
Can any body help me to understand this ...

Warning is
WARNING 2 [file gro.mdp]:
   The sum of the two largest charge group radii (5.930022) is larger than
   rlist (1.80)

and my .mdp file is



Something is inconsistent; your error message says rlist is 1.8, but your .mdp 
says it is 1.0.


Regardless, either you have some very nasty charge groups (way too large) or you 
simply have groups broken across PBC, which is not actually a problem.  Recent 
versions of grompp are smart enough to deal with PBC, so this would only show up 
with an old version of Gromacs.


http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

-Justin


; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include  =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 0
; For exact run continuation or redoing part of a run
init_step= 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1

; number of steps for center of mass motion removal
nstcomm  = 10

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 100
nstcalcenergy= -1
nstenergy= 100
; Output frequency and precision for .xtc file
nstxtcout= 0
xtc-precision= 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns-type  = Grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1
; long-range cut-off for switched potentials
rlistlong= -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 80
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1

Re: [gmx-users] mdrun error

2014-05-17 Thread Mark Abraham

Your simulation seems too small to parallelize in the way you/mdrun tried.
But we need more information to be sure.

Mark
On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote:

 Hi Everyone 
 I need some help. With my mdrun command I am getting this following error
  .

 Program mdrun, VERSION 4.6.5
 Source code file:
 /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line:
 722

 Fatal error:
 DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via
 constraints from the neighboring cells. This probably means your constraint
 lengths are too long compared to the domain decomposition cell size.
 Decrease the number of domain decomposition grid cells or lincs-order.
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---

 Please help me to understand this error.What this error is all about ?
 Where should I search to resolve this error ?

 Thanks
 Lovika
 --
 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] mdrun error

2014-05-17 Thread Lovika Moudgil

Thanks for quick reply Mark...what information you are asking for?Should I
search for this my .mdp file??

Thanks
 Lovika


On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Your simulation seems too small to parallelize in the way you/mdrun tried.
 But we need more information to be sure.

 Mark
 On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote:

  Hi Everyone 
  I need some help. With my mdrun command I am getting this following error
   .
 
  Program mdrun, VERSION 4.6.5
  Source code file:
  /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line:
  722
 
  Fatal error:
  DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via
  constraints from the neighboring cells. This probably means your
 constraint
  lengths are too long compared to the domain decomposition cell size.
  Decrease the number of domain decomposition grid cells or lincs-order.
  For more information and tips for troubleshooting, please check the
 GROMACS
  website at http://www.gromacs.org/Documentation/Errors
  ---
 
  Please help me to understand this error.What this error is all about ?
  Where should I search to resolve this error ?
 
  Thanks
  Lovika
  --
  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.

-- 
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] mdrun error

2014-05-17 Thread Mark Abraham

No, the .mdp file mostly describes your model physics (but there are some
implementation details that affect parallelization in there).

Your GROMACS CMake configuration, mdrun command line and the attributes of
your hardware are the biggest factors that determine how mdrun will try to
parallelise. There's a lot of diagnostic reporting in the log file, but you
are initially looking for the number of cells in the domain decomposition
(DD). And you need to know how big your simulation system is. For example,
a 900-molecule water system won't parallelise over a whole 32-core compute
server with a domain per core. Background info here
http://www.gromacs.org/Documentation/Acceleration_and_parallelization

Mark


On Sat, May 17, 2014 at 9:02 AM, Lovika Moudgil lovikamoud...@gmail.comwrote:

 Thanks for quick reply Mark...what information you are asking for?Should I
 search for this my .mdp file??

 Thanks
  Lovika


 On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  Your simulation seems too small to parallelize in the way you/mdrun
 tried.
  But we need more information to be sure.
 
  Mark
  On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com
 wrote:
 
   Hi Everyone 
   I need some help. With my mdrun command I am getting this following
 error
.
  
   Program mdrun, VERSION 4.6.5
   Source code file:
   /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c,
 line:
   722
  
   Fatal error:
   DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via
   constraints from the neighboring cells. This probably means your
  constraint
   lengths are too long compared to the domain decomposition cell size.
   Decrease the number of domain decomposition grid cells or lincs-order.
   For more information and tips for troubleshooting, please check the
  GROMACS
   website at http://www.gromacs.org/Documentation/Errors
   ---
  
   Please help me to understand this error.What this error is all about ?
   Where should I search to resolve this error ?
  
   Thanks
   Lovika
   --
   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.
 
 --
 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] mdrun error

2014-05-17 Thread Lovika Moudgil

Mark thanks for your reply and support . [?]

Regards
Lovika


On Sat, May 17, 2014 at 5:23 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 No, the .mdp file mostly describes your model physics (but there are some
 implementation details that affect parallelization in there).

 Your GROMACS CMake configuration, mdrun command line and the attributes of
 your hardware are the biggest factors that determine how mdrun will try to
 parallelise. There's a lot of diagnostic reporting in the log file, but you
 are initially looking for the number of cells in the domain decomposition
 (DD). And you need to know how big your simulation system is. For example,
 a 900-molecule water system won't parallelise over a whole 32-core compute
 server with a domain per core. Background info here
 http://www.gromacs.org/Documentation/Acceleration_and_parallelization

 Mark


 On Sat, May 17, 2014 at 9:02 AM, Lovika Moudgil lovikamoud...@gmail.com
 wrote:

  Thanks for quick reply Mark...what information you are asking for?Should
 I
  search for this my .mdp file??
 
  Thanks
   Lovika
 
 
  On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.com
  wrote:
 
   Your simulation seems too small to parallelize in the way you/mdrun
  tried.
   But we need more information to be sure.
  
   Mark
   On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com
  wrote:
  
Hi Everyone 
I need some help. With my mdrun command I am getting this following
  error
 .
   
Program mdrun, VERSION 4.6.5
Source code file:
/home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c,
  line:
722
   
Fatal error:
DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected
 via
constraints from the neighboring cells. This probably means your
   constraint
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or
 lincs-order.
For more information and tips for troubleshooting, please check the
   GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
   
Please help me to understand this error.What this error is all about
 ?
Where should I search to resolve this error ?
   
Thanks
Lovika
--
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-usersor
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.
  
  --
  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.

-- 
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] mdrun error

2014-05-16 Thread Lovika Moudgil

Hi Everyone 
I need some help. With my mdrun command I am getting this following error  .

Program mdrun, VERSION 4.6.5
Source code file:
/home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line:
722

Fatal error:
DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or lincs-order.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Please help me to understand this error.What this error is all about ?
Where should I search to resolve this error ?

Thanks
Lovika
-- 
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.

42 matches

Mail list logo