date:20100614




fancy2012 wrote:

Dear all,
Thanks very much for Justin A. Lemkul's explanations! I have got the idea.
I have a problem of my mailing list, I can't receive the independent 
mails from mailing list as before. I can only get the Digest, is there 
something wrong with my e-mail box? Thanks very much!


There's nothing wrong, you just chose digest when you subscribed.  Change your 
settings here:


http://lists.gromacs.org/mailman/listinfo/gmx-users

Also, if you instead decide to keep receiving digests, please pay attention to 
this information posted in every message:


When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."

...and also cut and paste only the relevant text.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] position restraint....NEED URGENT HELP




nikhil damle wrote:

Hey !

My doubt posted few days back still holds. I am trying to simulate the 
kinase domain in complex with cyclin. when i keep entire complex either 
position restrained or flexible, MD runs without any errors. But as soon 
as i keep cyclin position restrained keeping kinase domain flexible, it 
gives errors.


Initially it gave LINCS warnings saying fatal error that charged group 
at atom xx moved more than distance allowed by DD in direction X. 
Error persists even if i repeat the same procedure this time 
equilibrating the system for 150ps instead of usual 40ps. the pdb file 
obtained after equilibration appears perfect without any breaks.


As suggested by Justin, I also tried to check if my system is blowing 
up. But when i take co-ordinates of last frame, i get few random 
fragments having no 3D structure/ interconnections.




That is not what I suggested.  I said to watch the trajectory to see where it 
starts to break down.  If it's already broken, you can't see where the problems 
started.  Also:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


Here is .top file that i am using:






rlist = 2.0
coulombtype = PME
rcoulomb = 2.0; in nm units
vdwtype = cut-off
rvdw = 2.0







I wish to do MD with increased electrostatic and VdW cut-offs. Chain B 
is Cyclin and A is kinase domain.




Why do you wish to increase the cutoffs?  For rvdw especially, you may be 
seriously breaking the force field.


If you're restraining one species and altering the nature of the surrounding 
interactions, you may be preserving or creating clashes that cannot be resolved 
because of the restraints.  See the above link for tips on how to better 
diagnose what's going on.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] xpm file

2010-06-14 Thread Carla Jamous

Hi everyone,

please it's been two days that I can't have access to search the mailing
list. Maybe there is a problem. So please can anyone help me?

I used the g_covar and got covar.xpm file. My problem is that I can't figure
out which application can open the xpm file, so I converted it to .eps file
& opened it with Gimp, but the quality of the colours is really bad & so I
can't see much to analyse the graph.

Please has anyone encountered this problem before?

Thanks,
Carla
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] the box lengths

 Hi,

First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off length. 
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in the editconf 
about the box size, actually this box is really large enough for the testing 
consideration, but still has the same problem.

integrator  = steep
emtol   = 1.0
nsteps  = 500
nstenergy   = 1
energygrps  = System

ns_type = simple
coulombtype = cut-off
rcoulomb= 1.0
rvdw= 1.0
constraints = none
pbc = xyz

Thanks for any advice,

Best regards,

lina

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] the box lengths




#ZHAO LINA# wrote:

 Hi,

First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off length. 
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in the 
editconf about the box size, actually this box is really large enough 
for the testing consideration, but still has the same problem.




Well, what are your box vectors?  If they are < 2 nm, you will get this error 
because of the minimum image convention.


http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin


integrator  = steep
emtol   = 1.0
nsteps  = 500
nstenergy   = 1
energygrps  = System

ns_type = simple
coulombtype = cut-off
rcoulomb= 1.0
rvdw= 1.0
constraints = none
pbc = xyz

Thanks for any advice,

Best regards,

lina



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths

___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:
>  Hi,
>
> First time I meet this problem,
> ERROR: One of the box lengths is smaller than twice the cut-off length.
> Increase the box size or decrease rlist.
> I just followed the advice increase the box size, I tried twice in the
> editconf about the box size, actually this box is really large enough
> for the testing consideration, but still has the same problem.
>

Well, what are your box vectors?  If they are < 2 nm, you will get this error
because of the minimum image convention.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin

system size :  4.581  2.380  2.715 (nm)
diameter:  4.889   (nm)
center  : -0.012  0.003 -0.904 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  9.678  9.664  5.461 (nm)
new center  :  9.667  9.667  4.557 (nm)
new box vectors : 12.889 12.889 12.889 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1514.05   (nm^3)

This one I set was really large, but still showed that problems.

Thanks,

lina


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

 Hi,

First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in the
editconf about the box size, actually this box is really large enough
for the testing consideration, but still has the same problem.

Well, what are your box vectors?  If they are < 2 nm, you will get this error
because of the minimum image convention.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin

system size :  4.581  2.380  2.715 (nm)
diameter:  4.889   (nm)
center  : -0.012  0.003 -0.904 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  9.678  9.664  5.461 (nm)
new center  :  9.667  9.667  4.557 (nm)
new box vectors : 12.889 12.889 12.889 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1514.05   (nm^3)

This one I set was really large, but still showed that problems.

What problems?  The same error about the box lengths being shorter than twice 
the cutoff?  I don't think that's possible, given those vectors, if you're 
keeping your cutoffs at 1.0 nm.

-Justin

Thanks,

lina

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] moleculetype CU1+ is redefined

2010-06-14 Thread afsaneh maleki

 Hi,
When I generate the tpr file with grompp, I get the following error.
"Fatal error: moleculetype CU1+ is redefined"
I work on membrane protein that have no atomtype CU1+. why i get error on
CU+?
I have cheked [moleculetypes]  in toplogy file and there  are n't
doplicated.
How to remove this error?

thanks in advance,
Afsaneh
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:
> ___
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Monday, June 14, 2010 9:33 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] the box lengths
>
> #ZHAO LINA# wrote:
>>  Hi,
>>
>> First time I meet this problem,
>> ERROR: One of the box lengths is smaller than twice the cut-off length.
>> Increase the box size or decrease rlist.
>> I just followed the advice increase the box size, I tried twice in the
>> editconf about the box size, actually this box is really large enough
>> for the testing consideration, but still has the same problem.
>>
>
> Well, what are your box vectors?  If they are < 2 nm, you will get this error
> because of the minimum image convention.
>
> http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
>
> -Justin
>
> system size :  4.581  2.380  2.715 (nm)
> diameter:  4.889   (nm)
> center  : -0.012  0.003 -0.904 (nm)
> box vectors :  0.000  0.000  0.000 (nm)
> box angles  :   0.00   0.00   0.00 (degrees)
> box volume  :   0.00   (nm^3)
> shift   :  9.678  9.664  5.461 (nm)
> new center  :  9.667  9.667  4.557 (nm)
> new box vectors : 12.889 12.889 12.889 (nm)
> new box angles  :  60.00  60.00  90.00 (degrees)
> new box volume  :1514.05   (nm^3)
>
> This one I set was really large, but still showed that problems.
>

What problems?  The same error about the box lengths being shorter than twice
the cutoff?  I don't think that's possible, given those vectors, if you're
keeping your cutoffs at 1.0 nm.

-Justin

I do keep the cut-off. That's I do not know why. Four times had been tried. 

> Thanks,
>
> lina
>
>
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

 Hi,

First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in the
editconf about the box size, actually this box is really large enough
for the testing consideration, but still has the same problem.

Well, what are your box vectors?  If they are < 2 nm, you will get this error
because of the minimum image convention.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin

system size :  4.581  2.380  2.715 (nm)
diameter:  4.889   (nm)
center  : -0.012  0.003 -0.904 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  9.678  9.664  5.461 (nm)
new center  :  9.667  9.667  4.557 (nm)
new box vectors : 12.889 12.889 12.889 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1514.05   (nm^3)

This one I set was really large, but still showed that problems.

What problems?  The same error about the box lengths being shorter than twice
the cutoff?  I don't think that's possible, given those vectors, if you're
keeping your cutoffs at 1.0 nm.

-Justin

I do keep the cut-off. That's I do not know why. Four times had been tried. 

Are you using the right files?  You're not repeating the same commands with the 
zero-box length vectors (which was the source of your problem in the first 
place)?  There is absolutely no reason you'd get an error with 1.0-nm cutoffs 
and > 12 nm box vectors.

-Justin

Thanks,

lina

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] moleculetype CU1+ is redefined




afsaneh maleki wrote:

Hi,
When I generate the tpr file with grompp, I get the following error.
"Fatal error: moleculetype CU1+ is redefined"
I work on membrane protein that have no atomtype CU1+. why i get error 
on CU+?
I have cheked [moleculetypes]  in toplogy file and there  are n't 
doplicated.

How to remove this error?



You have probably #included some topology twice, wherein CU1+ is defined.  Maybe 
ions.itp?  Check your topology carefully.


-Justin


thanks in advance,
Afsaneh



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] question about [ pairs ] and interaction 1-4

2010-06-14 Thread Alan

Hi there,

I mostly use ffamber and sometimes I look in oplsaa to understand how things
are implemented in gromacs (4.0.5)

I have an example here, where 2 atoms, in a phosphate (see
http://en.wikipedia.org/wiki/File:1-hydrogenphosphate-3D-balls.png) in 1-4
interaction that have opposite charges (0.473 x -0.787) and when doing a EM,
the H will move towards and basically join one of the Oxygen of the
phosphate (coulomb force clearly acting, but no LJ repulsion?).

The definitions in the top file are:

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ pairs ]
;   ai ajfunct
 1  4  1 ;HHO - O01

What I was expecting is since I declared the pair 1, 4 in [ pairs ]  and the
parameters to be set 0 by omission (or am wrong here?) that such interaction
between atoms HHO and O01 shouldn't happen, but clearly it's not what I see.

Yet I checked the manual, page 112 in particular.

It is the first time I come across an example where I have 2 atom in 1-4
interaction with such a large opposite charges.

Is the behaviour I see OK, although apparently rare?

Many thanks in advance,

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: the box lengths

2010-06-14 Thread Vitaly Chaban

> First time I meet this problem,
> ERROR: One of the box lengths is smaller than twice the cut-off length. 
> Increase the box size or decrease rlist.
> I just followed the advice increase the box size, I tried twice in the 
> editconf about the box size, actually this box is really large enough for the 
> testing consideration, but still has the same problem.

Lina -

Which moment are you experiencing this problem at?


Good luck.

Dr. Vitaly Chaban
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] ions.itp

2010-06-14 Thread afsaneh maleki

Dear justin,
thanks for your helpful reply.

where Gromacs does not have a force field of its own, but is compatible with
GROMOS, OPLS, AMBER, and
ENCAD force fields. why in "ions.itp"   #ifdef _FF_GROMACS is defended?

Best wishes,
Afsaneh Maleki
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: moleculetype CU1+ is redefined

2010-06-14 Thread Vitaly Chaban

> When I generate the tpr file with grompp, I get the following error.
> "Fatal error: moleculetype CU1+ is redefined"
> I work on membrane protein that have no atomtype CU1+. why i get error on
> CU+?
> I have cheked [moleculetypes]  in toplogy file and there  are n't
> doplicated.
> How to remove this error?

How many FF files have you included into the topology file?


Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] ions.itp




afsaneh maleki wrote:

Dear justin,
thanks for your helpful reply.

where Gromacs does not have a force field of its own, but is compatible 
with GROMOS, OPLS, AMBER, and

ENCAD force fields. why in "ions.itp"   #ifdef _FF_GROMACS is defended?


This corresponds to ffgmx (a deprecated Gromos87 with some manual hacks).

-Justin

 
Best wishes,

Afsaneh Maleki



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Re: moleculetype CU1+ is redefined

2010-06-14 Thread afsaneh maleki

this error is removed. becuse "ion.itp"was included twice in .top and .itp
files.
i have included two FF into topology file, one for protein and another one
for bilayer.

Afsaneh

On Mon, Jun 14, 2010 at 6:07 PM, Vitaly Chaban  wrote:

> > When I generate the tpr file with grompp, I get the following error.
> > "Fatal error: moleculetype CU1+ is redefined"
> > I work on membrane protein that have no atomtype CU1+. why i get error on
> > CU+?
> > I have cheked [moleculetypes]  in toplogy file and there  are n't
> > doplicated.
> > How to remove this error?
>
> How many FF files have you included into the topology file?
>
>
> Dr. Vitaly Chaban
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

2010-06-14 Thread Godwin Kanu



Hi,

 

I stopped removing center of mass motion as advised by Tsjerk, but I experience 
the same problem still. I understand the arguement of subtracting out the 
momentum, but if this was the sole issue, I should experience the same problem 
when simulating pure liquids, but I don't. Any more suggestions will be 
appreciated. 

 

Godwin

 



 
> Date: Mon, 14 Jun 2010 11:55:18 +0200
> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of liquid 
> mixtures
> From: tsje...@gmail.com
> To: gmx-users@gromacs.org
> 
> Hey :)
> 
> Errm, you subtract the overall linear momentum. That affects the
> kinetic energy, decreasing it, doesn't it?
> 
> Tsjerk
> 
> On Mon, Jun 14, 2010 at 10:59 AM, Berk Hess  wrote:
> > Hi,
> >
> > Why not?
> >
> > Berk
> >
> >> Date: Mon, 14 Jun 2010 08:19:30 +0200
> >> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of
> >> liquid mixtures
> >> From: tsje...@gmail.com
> >> To: gmx-users@gromacs.org
> >>
> >> Hi Godwin,
> >>
> >> I noticed you're removing center of mass motion, which you shouldn't for
> >> NVE.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu  wrote:
> >> >
> >> > Hi GMX Users,
> >> >
> >> > I am having difficulties getting gromacs to conserve energy (I
> >> > experience a
> >> > directional drift) when I do an NVE simulation of mixtures (i tried both
> >> > THF/water and water/methanol). But when I do simulation of a pure liquid
> >> > it
> >> > works great. I have tried tinkering with a lot of stuff including the
> >> > electrostatic interaction and making sure the combination rules for
> >> > non-bonded interactions work as it is supposed to. I usually start with
> >> > an
> >> > NVT simulation to equilibriate it at the temperature I'm interested in
> >> > before removing the temperature bath to do an equilibration run in
> >> > the microcanonical ensemble. I have attached some of my input files for
> >> > you
> >> > to examine. I'm using GROMACS version 4.0.5 parallel.
> >> > Thanks
> >> >
> >> > Godwin.
> >> >
> >> >
> >> >
> >> > 
> >> > Hotmail has tools for the New Busy. Search, chat and e-mail from your
> >> > inbox.
> >> > Learn more.
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.gromacs.org/search before
> >> > posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> Groningen Institute for Biomolecular Research and Biotechnology
> >> University of Groningen
> >> The Netherlands
> >> --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > 
> > New Windows 7: Find the right PC for you. Learn more.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
> -- 
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
  
_
Hotmail is redefining busy with tools for the New Busy. Get more from your 
inbox.
http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.

RE: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

2010-06-14 Thread Berk Hess


Yes, but that is done before starting the simulation, so your total energy
will still be nicely constant.

Berk

> Date: Mon, 14 Jun 2010 11:55:18 +0200
> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of liquid   
> mixtures
> From: tsje...@gmail.com
> To: gmx-users@gromacs.org
> 
> Hey :)
> 
> Errm, you subtract the overall linear momentum. That affects the
> kinetic energy, decreasing it, doesn't it?
> 
> Tsjerk
> 
> On Mon, Jun 14, 2010 at 10:59 AM, Berk Hess  wrote:
> > Hi,
> >
> > Why not?
> >
> > Berk
> >
> >> Date: Mon, 14 Jun 2010 08:19:30 +0200
> >> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of
> >> liquid mixtures
> >> From: tsje...@gmail.com
> >> To: gmx-users@gromacs.org
> >>
> >> Hi Godwin,
> >>
> >> I noticed you're removing center of mass motion, which you shouldn't for
> >> NVE.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu  wrote:
> >> >
> >> > Hi GMX Users,
> >> >
> >> > I am having difficulties getting gromacs to conserve energy (I
> >> > experience a
> >> > directional drift) when I do an NVE simulation of mixtures (i tried both
> >> > THF/water and water/methanol). But when I do simulation of a pure liquid
> >> > it
> >> > works great. I have tried tinkering with a lot of stuff including the
> >> > electrostatic interaction and making sure the combination rules for
> >> > non-bonded interactions work as it is supposed to. I usually start with
> >> > an
> >> > NVT simulation to equilibriate it at the temperature I'm interested in
> >> > before removing the temperature bath to do an equilibration run in
> >> > the microcanonical ensemble. I have attached some of my input files for
> >> > you
> >> > to examine. I'm using GROMACS version 4.0.5 parallel.
> >> > Thanks
> >> >
> >> > Godwin.
> >> >
> >> >
> >> >
> >> > 
> >> > Hotmail has tools for the New Busy. Search, chat and e-mail from your
> >> > inbox.
> >> > Learn more.
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.gromacs.org/search before
> >> > posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> Groningen Institute for Biomolecular Research and Biotechnology
> >> University of Groningen
> >> The Netherlands
> >> --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > 
> > New Windows 7: Find the right PC for you. Learn more.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
  
_
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Re: moleculetype CU1+ is redefined

2010-06-14 Thread Lucio Ricardo Montero Valenzuela

You should be careful working with two force fields. They have to be compatible.
See
http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization&highlight=mix.
Mensaje citado por afsaneh maleki :

> this error is removed. becuse "ion.itp"was included twice in .top and .itp
> files.
> i have included two FF into topology file, one for protein and another one
> for bilayer.
>
> Afsaneh
>
> On Mon, Jun 14, 2010 at 6:07 PM, Vitaly Chaban  wrote:
>
> > > When I generate the tpr file with grompp, I get the following error.
> > > "Fatal error: moleculetype CU1+ is redefined"
> > > I work on membrane protein that have no atomtype CU1+. why i get error on
> > > CU+?
> > > I have cheked [moleculetypes]  in toplogy file and there  are n't
> > > doplicated.
> > > How to remove this error?
> >
> > How many FF files have you included into the topology file?
> >
> >
> > Dr. Vitaly Chaban
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>


-- 
Lucio Ricardo Montero Valenzuela
Estudiante de doctorado en Ciencias Bioquímicas
Lab. del Dr. Federico Sánchez
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico


Este mensaje fue enviado desde el servidor Webmail del Instituto de 
Biotecnologia.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Positive Total energy

2010-06-14 Thread Thanasis Koukoulas

Hello
I have sent several emails and i am sorry. It is my last attempt to finish this
simulation.The molecule i have is C-C-C-C-C-C-O-C-C-O-C-C-O-H or C10H1O3. (ciej
molecule)
I dont use gromacs librariesthe files i use are attached to the email in which
i have descriped step by step the forcefield i use. as you can see in [pairs] i
have an extra non Lj 1-4 pair. i did it because the model i use has a potential
between atom 10 and 14 ether oxygen and alchohol hydrogen interaction. It is
described in the paper as a repulsive energy between these two atoms. and it
has a formula:
Erepulsive = 3.325789e-7/r^12
the only way to import in gromacs i think is this:
[ pairs ]; ai aj funct 10 14 2 0 0 0 0 3.325789e-7
it is an intra-molecular only interaction. so i couldnt think another way to do
it except this. as you can see i have several zeros for the charges, C6=o and
C12 = 3.325789e-7 fidgeQQ=0 for this case
the problem is i get positive total energy. i did this sim for only one
molecule just to see what is wrong and i think that coulomb (SR) are wrong for
sure.
so i want
coulomb 1-4 /2 !thats why i put fudgeQQ = 0.5
the values i get at the step 0 are
Energies (kJ/mol) Angle Proper Dih. LJ-14 Coulomb-14
LJ (SR) 2.30340e+03 1.08417e+00 3.16570e+00 8.79204e+04
-2.54164e+03 Disper. corr. Coulomb (SR) Coul. recip. Potential
Kinetic En. -2.51250e+00 -4.81042e+04 -2.84931e+04 1.10867e+04
1.84852e+04 Total Energy Temperature Pressure (bar) Cons. rmsd ()
2.95719e+04 2.99528e+02 -3.03583e+02 3.13477e-06
tell me please how is this possible
thanks in advance and i am sorry once again

ciejbon.itp
Description: Binary data

ciejnb.itp
Description: Binary data

ciej.itp
Description: Binary data

ciej.top
Description: Binary data
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Disk Space

2010-06-14 Thread teklebrh


Dear Chris,

Thank you very much!

I am planning to set the output control option like this!

tinit   =  0
nstxout =  2000
nstvout =  0
nstfout =  0
nstlog  =  2000
nstenergy   =  1000

I want to set the velocity and force option to zero and save the  
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By doing  
this am I missing anything.


regards,

Rob



Quoting chris.ne...@utoronto.ca:


Dear Rob:

To answer your question: just set up your run with nsteps for 5 ns,  
run mdrun, and then use tpbconv -until. A simpler option is to set  
it up to run 20 ns, but use -maxh to limit it to an amount of  
runtime that you pre-calculate to be similar to 5 ns of simulation.


HOWEVER:

You almost surely don't need to save this so often: nstxout = 100  
(also nstvout, nstfout).


And you may not even need to save this so often: nstxtcout = 100  
(also nstenergy).


I had no idea that there was an option nstcheckpoint = 100 as I use  
mdrun -cpt 6 to specify a .cpt file every 6 hours, but there is no  
need to write a .cpt every 100 steps.




Dear Gromacs users,

I am running an MD simulation but it looks to me that I am running out
of disk space.

This is my .mdp file

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 100
; Output frequency for energies to log file and energy file
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file
nstxtcout= 100
xtc-precision= 100
nstcheckpoint= 100 ; checkpointing helps you continue
after crashe. This checkpint file is saved every 1ns


Please tell me which files i need to set zero.

I am planning to run my simulation for 20ns but I want it to run every
five nanoseconds until i see an aggregations in my system. So how can
I re-start my simulation every 5ns.


Thank you for your help

rob



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use thewww  
interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Disk Space




tekle...@ualberta.ca wrote:

Dear Chris,

Thank you very much!

I am planning to set the output control option like this!

tinit   =  0
nstxout =  2000
nstvout =  0
nstfout =  0
nstlog  =  2000
nstenergy   =  1000

I want to set the velocity and force option to zero and save the 
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By doing 
this am I missing anything.




Unless you need full-precision coordinates every few ps, you can use nstxtcout = 
2000 and set nstxout = 0.  A .xtc file is substantially smaller than a .trr file.


-Justin


regards,

Rob



Quoting chris.ne...@utoronto.ca:


Dear Rob:

To answer your question: just set up your run with nsteps for 5 ns, 
run mdrun, and then use tpbconv -until. A simpler option is to set it 
up to run 20 ns, but use -maxh to limit it to an amount of runtime 
that you pre-calculate to be similar to 5 ns of simulation.


HOWEVER:

You almost surely don't need to save this so often: nstxout = 100 
(also nstvout, nstfout).


And you may not even need to save this so often: nstxtcout = 100 (also 
nstenergy).


I had no idea that there was an option nstcheckpoint = 100 as I use 
mdrun -cpt 6 to specify a .cpt file every 6 hours, but there is no 
need to write a .cpt every 100 steps.




Dear Gromacs users,

I am running an MD simulation but it looks to me that I am running out
of disk space.

This is my .mdp file

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 100
; Output frequency for energies to log file and energy file
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file
nstxtcout= 100
xtc-precision= 100
nstcheckpoint= 100 ; checkpointing helps you continue
after crashe. This checkpint file is saved every 1ns


Please tell me which files i need to set zero.

I am planning to run my simulation for 20ns but I want it to run every
five nanoseconds until i see an aggregations in my system. So how can
I re-start my simulation every 5ns.


Thank you for your help

rob



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before 
posting!
Please don't post (un)subscribe requests to the list. Use thewww 
interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Disk Space

2010-06-14 Thread chris . neale

a question like "is this much really enough?" is impossible for me to  
answer. I suggest that you look at the autocorrelation times of your  
observables and perhaps (very likely actually) you will realize that  
you don't need to save nearly as often as you are saving.


Also, read the manual about nstxout and nstxtcout. I don;t even use  
the .trr file anymore and very likely it is becoming obsolete for a  
lot of users.


Chris.

-- original message --

Dear Chris,

Thank you very much!

I am planning to set the output control option like this!

tinit   =  0
nstxout =  2000
nstvout =  0
nstfout =  0
nstlog  =  2000
nstenergy   =  1000

I want to set the velocity and force option to zero and save the
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By doing
this am I missing anything.

regards,

Rob

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Disk Space

2010-06-14 Thread teklebrh


Dear Chris and Justin,

I just read the manual and it stated that I need a .trr file if I want  
to extend the simulation ( from 5ns -20ns).


My question is:

For the first 5ns I want to use berendsen thermostat and barostat so  
that my system will relax faster compared to N-H and P-R. Then I will  
switch on to the Nose-Hover and Parrinello-Rahman ( this will give me  
a correct description for the kinetic energy information.


Therefore, I need both coordinate and velocity files then ( Gromacs 3.3.3).


nstxout  = 5
nstvout  = 5
nstfout  = 0



; Output frequency for energies to log file and energy file
nstlog   = 2000
nstenergy= 1000
; Output frequency and precision for xtc file
nstxtcout= 2000
xtc-precision= 1000


rather than set the values of nstxout and  nstvout , if I set them to  
5, I could get the .trr file. But for my entire analysis I will  
depend on the .xtc file.


step 1

after 5ns of my simulation( Both berendsen thermostat and barostat. I  
have to use still grompp to generate a new .tpr file by modifying the  
.mdp file ( t_ coupling,p_couple and the tinit). Once done this I run  
mdrun.


step 2

use the following procedure then after

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr  
-extend timetoextend


Am I correct? and also is the output file seems reasonable.

I am trying to balance both the disk space issue and what output I  
need to continue further.


Thank you chris and justine.

Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Chris,

Thank you very much!

I am planning to set the output control option like this!

tinit   =  0
nstxout =  2000
nstvout =  0
nstfout =  0
nstlog  =  2000
nstenergy   =  1000

I want to set the velocity and force option to zero and save the  
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By  
doing this am I missing anything.




Unless you need full-precision coordinates every few ps, you can use  
nstxtcout = 2000 and set nstxout = 0.  A .xtc file is substantially  
smaller than a .trr file.


-Justin


regards,

Rob



Quoting chris.ne...@utoronto.ca:


Dear Rob:

To answer your question: just set up your run with nsteps for 5  
ns, run mdrun, and then use tpbconv -until. A simpler option is to  
set it up to run 20 ns, but use -maxh to limit it to an amount of  
runtime that you pre-calculate to be similar to 5 ns of simulation.


HOWEVER:

You almost surely don't need to save this so often: nstxout = 100  
(also nstvout, nstfout).


And you may not even need to save this so often: nstxtcout = 100  
(also nstenergy).


I had no idea that there was an option nstcheckpoint = 100 as I  
use mdrun -cpt 6 to specify a .cpt file every 6 hours, but there  
is no need to write a .cpt every 100 steps.




Dear Gromacs users,

I am running an MD simulation but it looks to me that I am running out
of disk space.

This is my .mdp file

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 100
; Output frequency for energies to log file and energy file
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file
nstxtcout= 100
xtc-precision= 100
nstcheckpoint= 100 ; checkpointing helps you continue
after crashe. This checkpint file is saved every 1ns


Please tell me which files i need to set zero.

I am planning to run my simulation for 20ns but I want it to run every
five nanoseconds until i see an aggregations in my system. So how can
I re-start my simulation every 5ns.


Thank you for your help

rob



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use thewww  
interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www  
interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users

RE: [gmx-users] FEP for amino acid mutations.

I would make a new residue in the .rtp file.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Matteo De Chiara
> Sent: Monday, 14 June 2010 8:05 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] FEP for amino acid mutations.
> 
> Dear GROMACS users,
> I would like to perform a FEP calculation mutating a residue outside
> the active site of a protein.
> I was wondering if I have to create a .itp file for the mutation or it
> is possible to modify the .rtp file ( adding the state B parameter to
> the amino acid I would like to change). Of course, in this case, I
> will create a new amino acid type identical to the one I would like to
> mutate in order to act only on the amino acid in a specific position.
> 
> Thanks for your help!
> 
> matteo
> 
> 
> 
> --
> 
> Ph.D. Student
> Matteo De Chiara
> Dept. of Molecular Biology, University of Siena
> 
> Via Fiorentina 1,
> 53100 Siena Italy
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths

Please copy and paste in the commands you are using, and the output.

I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupling on. So when you
start the simulation, not surprising that the box compresses again and
goes under 2nm again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 12:04 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> 
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Monday, June 14, 2010 10:02 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] the box lengths
> 
> #ZHAO LINA# wrote:
> > ___
> > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
> on behalf of Justin A. Lemkul [jalem...@vt.edu]
> > Sent: Monday, June 14, 2010 9:33 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] the box lengths
> >
> > #ZHAO LINA# wrote:
> >>  Hi,
> >>
> >> First time I meet this problem,
> >> ERROR: One of the box lengths is smaller than twice the cut-off
> length.
> >> Increase the box size or decrease rlist.
> >> I just followed the advice increase the box size, I tried twice in
> the
> >> editconf about the box size, actually this box is really large
> enough
> >> for the testing consideration, but still has the same problem.
> >>
> >
> > Well, what are your box vectors?  If they are < 2 nm, you will get
> this error
> > because of the minimum image convention.
> >
> >
>
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
> on
> >
> > -Justin
> >
> > system size :  4.581  2.380  2.715 (nm)
> > diameter:  4.889   (nm)
> > center  : -0.012  0.003 -0.904 (nm)
> > box vectors :  0.000  0.000  0.000 (nm)
> > box angles  :   0.00   0.00   0.00 (degrees)
> > box volume  :   0.00   (nm^3)
> > shift   :  9.678  9.664  5.461 (nm)
> > new center  :  9.667  9.667  4.557 (nm)
> > new box vectors : 12.889 12.889 12.889 (nm)
> > new box angles  :  60.00  60.00  90.00 (degrees)
> > new box volume  :1514.05   (nm^3)
> >
> > This one I set was really large, but still showed that problems.
> >
> 
> What problems?  The same error about the box lengths being shorter
than
> twice
> the cutoff?  I don't think that's possible, given those vectors, if
> you're
> keeping your cutoffs at 1.0 nm.
> 
> -Justin
> 
> I do keep the cut-off. That's I do not know why. Four times had been
> tried.
> 
> > Thanks,
> >
> > lina
> >
> >
> >
> 
> --
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] anisotropic pressure coupling

2010-06-14 Thread Shuangxing Dai

Hi all:
I was using Parrinello-Rahman for pressure coupling and here is the mdp
file:

; RUN CONTROL PARAMETERS =
integrator   = sd
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 20
; number of steps for center of mass motion removal =
nstcomm  = 100
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 50
; ns algorithm (simple or grid) =
ns_type  = grid

;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = Parrinello-Rahman
pcoupltype   = anisotropic
tau_p= 1
compressibility  = 2.1645e-09  2.1645e-09 2.7322e-09 0 0 0
ref_p= 1 1 1 0 0 0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1
ref_t= 300
; OPTIONS FOR BONDS =
constraints  = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Relative tolerance of shake =
shake-tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order  = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle  = 30
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw = 1

; 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= 6
ewald_rtol   = 1e-4
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

 It seems that the temperature coupling is fast and fluctuation is less that
1%. But the pressure coupling fails. The pressure fluctuates from +1e3 bar
to -1e3 bar. Anyone can help?


Thanks,
Shuangxing Dai
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Disk Space




tekle...@ualberta.ca wrote:

Dear Chris and Justin,

I just read the manual and it stated that I need a .trr file if I want 
to extend the simulation ( from 5ns -20ns).


My question is:

For the first 5ns I want to use berendsen thermostat and barostat so 
that my system will relax faster compared to N-H and P-R. Then I will 
switch on to the Nose-Hover and Parrinello-Rahman ( this will give me a 
correct description for the kinetic energy information.


Therefore, I need both coordinate and velocity files then ( Gromacs 3.3.3).


nstxout  = 5
nstvout  = 5
nstfout  = 0



; Output frequency for energies to log file and energy file
nstlog   = 2000
nstenergy= 1000
; Output frequency and precision for xtc file
nstxtcout= 2000
xtc-precision= 1000


rather than set the values of nstxout and  nstvout , if I set them to 
5, I could get the .trr file. But for my entire analysis I will 
depend on the .xtc file.


step 1

after 5ns of my simulation( Both berendsen thermostat and barostat. I 
have to use still grompp to generate a new .tpr file by modifying the 
.mdp file ( t_ coupling,p_couple and the tinit). Once done this I run 
mdrun.


step 2

use the following procedure then after

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr 
-extend timetoextend


Am I correct? and also is the output file seems reasonable.



That's certainly a reasonable way to extend a simulation.  With 3.3.3, you need 
full-precision coordinates and velocities.  Is there any reason you want to use 
software that is several years old?  The upgrades in the 4.0.x series are quite 
nice, and make extending simulations far easier, requiring only a checkpoint 
file.  This (I assume) is why Chris said that the .trr file is becoming obsolete.


I am trying to balance both the disk space issue and what output I need 
to continue further.




If you only need the .trr file to continue your simulation, you only need the 
very last frame, so there is really no reason to save high-precision coordinates 
every few ps for 5 ns.  Your .trr file may exceed several GB in size, all for no 
reason!


-Justin


Thank you chris and justine.

Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Chris,

Thank you very much!

I am planning to set the output control option like this!

tinit   =  0
nstxout =  2000
nstvout =  0
nstfout =  0
nstlog  =  2000
nstenergy   =  1000

I want to set the velocity and force option to zero and save the 
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By 
doing this am I missing anything.




Unless you need full-precision coordinates every few ps, you can use 
nstxtcout = 2000 and set nstxout = 0.  A .xtc file is substantially 
smaller than a .trr file.


-Justin


regards,

Rob



Quoting chris.ne...@utoronto.ca:


Dear Rob:

To answer your question: just set up your run with nsteps for 5 ns, 
run mdrun, and then use tpbconv -until. A simpler option is to set 
it up to run 20 ns, but use -maxh to limit it to an amount of 
runtime that you pre-calculate to be similar to 5 ns of simulation.


HOWEVER:

You almost surely don't need to save this so often: nstxout = 100 
(also nstvout, nstfout).


And you may not even need to save this so often: nstxtcout = 100 
(also nstenergy).


I had no idea that there was an option nstcheckpoint = 100 as I use 
mdrun -cpt 6 to specify a .cpt file every 6 hours, but there is no 
need to write a .cpt every 100 steps.




Dear Gromacs users,

I am running an MD simulation but it looks to me that I am running out
of disk space.

This is my .mdp file

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 100
; Output frequency for energies to log file and energy file
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file
nstxtcout= 100
xtc-precision= 100
nstcheckpoint= 100 ; checkpointing helps you continue
after crashe. This checkpint file is saved every 1ns


Please tell me which files i need to set zero.

I am planning to run my simulation for 20ns but I want it to run every
five nanoseconds until i see an aggregations in my system. So how can
I re-start my simulation every 5ns.


Thank you for your help

rob



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before 
posting!
Please don't post (un)subscribe requests to the list. Use thewww 
interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.ph

Re: [gmx-users] anisotropic pressure coupling




Shuangxing Dai wrote:

Hi all:
I was using Parrinello-Rahman for pressure coupling and here is the 
mdp file:


; RUN CONTROL PARAMETERS =
integrator   = sd
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 20
; number of steps for center of mass motion removal =
nstcomm  = 100
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 50
; ns algorithm (simple or grid) =
ns_type  = grid

;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = Parrinello-Rahman
pcoupltype   = anisotropic
tau_p= 1
compressibility  = 2.1645e-09  2.1645e-09 2.7322e-09 0 0 0
ref_p= 1 1 1 0 0 0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1
ref_t= 300
; OPTIONS FOR BONDS =
constraints  = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Relative tolerance of shake =
shake-tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order  = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle  = 30
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths   
rvdw = 1


; 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= 6
ewald_rtol   = 1e-4
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

 It seems that the temperature coupling is fast and fluctuation is less 
that 1%. But the pressure coupling fails. The pressure fluctuates from 
+1e3 bar to -1e3 bar. Anyone can help?




I don't call that failure.  Depending on the size of your system, you can 
probably expect very wide fluctuations in the pressure.  Is the average correct?


http://www.gromacs.org/Documentation/Terminology/Pressure

-Justin



Thanks,
Shuangxing Dai



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] xpm file



- Original Message -
From: Carla Jamous 
Date: Monday, June 14, 2010 22:40
Subject: [gmx-users] xpm file
To: Discussion list for GROMACS users 

> Hi everyone,
> 
> please it's been two days that I can't have access to search the mailing 
> list. Maybe there is a problem. So please can anyone help me?
> 
> I used the g_covar and got covar.xpm file. My problem is that I can't figure 
> out which application can open the xpm file, so I converted it to .eps file & 
> opened it with Gimp, but the quality of the colours is really bad & so I 
> can't see much to analyse the graph.

Google's top hit for "xpm file" suggests the GIMP can read .xpm natively.

Mark

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84

2010-06-14 Thread Shuangxing Dai

Well, the final average pressure is not correct:

* **<==  ###  ==>*
* **<  A V E R A G E S  >*
* **<==  ###  ==>*
*
*
*   Energies (kJ/mol)*
*  Buck.ham (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
*
*1.60633e+06   -5.69243e+06   -3.45003e+06   -7.53612e+061.80719e+04
*
*   Total EnergyTemperature Pressure (bar)*
*   -7.51805e+063.62347e+021.11758e+04*
*
*
*
*
*   Pressure (bar)*
*1.21051e+04   -2.94017e-011.30456e+00*
*   -2.94017e-019.03597e+03   -8.10850e-01*
*1.30456e+00   -8.10850e-011.23863e+04*
*
*
*
*
* **<==  ###  ==>*
* **<  R M S - F L U C T U A T I O N S  >*
* **<==  ###  ==>*
*
*
*   Energies (kJ/mol)*
*  Buck.ham (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
*
*3.92376e+054.00326e+054.71365e+013.02978e+042.35039e+03
*
*   Total EnergyTemperature Pressure (bar)*
*3.01091e+044.71259e+011.71117e+05*
*
*
*
*
*   Pressure (bar)*
*1.82323e+054.91513e+023.07107e+02*
*4.91513e+022.02402e+053.13857e+02*
*3.07107e+023.13857e+021.30179e+05*
*
*
*Also the fluctuation is very large. I think 200ps is long enough. But still
I cannot find the equilibrium.*
*I do not know whether the parameters are wrong or I ran the anisotropic
pressure coupling wrong. Is *Parrinello-Rahman pressure coupling sensitive
to the initial pressure? I mean if the initial pressure ( in order of GPa),
object pressure is 1 bar ( 1e5 Pa).
*
*
Thanks,
Shuangxing Dai


On Mon, Jun 14, 2010 at 8:50 PM,  wrote:
>
>
> Message: 3
> Date: Mon, 14 Jun 2010 19:18:14 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] anisotropic pressure coupling
> To: Discussion list for GROMACS users 
> Message-ID: <4c16b8b6.4010...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> Shuangxing Dai wrote:
> > Hi all:
> > I was using Parrinello-Rahman for pressure coupling and here is the
> > mdp file:
> >
> > ; RUN CONTROL PARAMETERS =
> > integrator   = sd
> > ; start time and timestep in ps =
> > tinit= 0
> > dt   = 0.001
> > nsteps   = 20
> > ; number of steps for center of mass motion removal =
> > nstcomm  = 100
> > ; NEIGHBORSEARCHING PARAMETERS =
> > ; nblist update frequency =
> > nstlist  = 50
> > ; ns algorithm (simple or grid) =
> > ns_type  = grid
> >
> > ;OPTIONS FOR PRESSURE COUPLING
> > Pcoupl   = Parrinello-Rahman
> > pcoupltype   = anisotropic
> > tau_p= 1
> > compressibility  = 2.1645e-09  2.1645e-09 2.7322e-09 0 0 0
> > ref_p= 1 1 1 0 0 0
> > ;OPTIONS FOR TEMPERATURE COUPLING
> > tc_grps  = system
> > tau_t= 0.1
> > ref_t= 300
> > ; OPTIONS FOR BONDS =
> > constraints  = hbonds
> > ; Type of constraint algorithm =
> > constraint-algorithm = Lincs
> > ; Do not constrain the start configuration =
> > unconstrained-start  = no
> > ; Relative tolerance of shake =
> > shake-tol= 0.0001
> > ; Highest order in the expansion of the constraint coupling matrix =
> > lincs-order  = 12
> > ; Lincs will write a warning to the stderr if in one step a bond =
> > ; rotates over more degrees than =
> > lincs-warnangle  = 30
> > ; Periodic boundary conditions: xyz, no, xy
> > pbc  = xyz
> > periodic_molecules   = no
> > ; nblist cut-off
> > rlist= 1
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype  = PME
> > rcoulomb = 1
> > ; Method for doing Van der Waals
> > vdw-type = Cut-off
> > ; cut-off lengths
> > rvdw = 1
> >
> > ; 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= 6
> > ewald_rtol   = 1e-4
> > ewald_geometry   = 3d
> > epsilon_surface  = 0
> > optimize_fft = no
> >
> >  It seems that the temperature coupling is fast and fluctuation is less
> > that 1%. But the pressure coupling fails. The pressure fluctuates from
> > +1e3 bar to -1e3 bar. Anyone can help?
> >
>
> I don't call that failure.  Depending on the size of your system, you can
> probably expect very wide fluctuations in the pressure.  Is the average
> correct?
>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> -Justin
>
> >
> > Thanks,
> > Shuangxing Dai
> >
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Can

Re: [gmx-users] question about [ pairs ] and interaction 1-4



- Original Message -
From: Alan 
Date: Tuesday, June 15, 2010 0:22
Subject: [gmx-users] question about [ pairs ] and interaction 1-4
To: Gromacs 

> Hi there,
> I mostly use ffamber and sometimes I look in oplsaa to understand how things 
> are implemented in gromacs (4.0.5)> 
> I have an example here, where 2 atoms, in a phosphate (see 
> http://en.wikipedia.org/wiki/File:1-hydrogenphosphate-3D-balls.png) in 1-4 
> interaction that have opposite charges (0.473 x -0.787) and when doing a EM, 
> the H will move towards and basically join one of the Oxygen of the phosphate 
> (coulomb force clearly acting, but no LJ repulsion?).  > 
> The definitions in the top file are:> 
> [ defaults ]> ; nbfunccomb-rule   gen-pairs   fudgeLJ 
> fudgeQQ> 1   2   yes 0.5 0.8333  > 
> [ pairs ]> ;   ai ajfunct>  1  4  1 ;HHO - O01   > 
> What I was expecting is since I declared the pair 1, 4 in [ pairs ]  and the 
> parameters to be set 0 by omission (or am wrong here?) that such interaction 
> between atoms HHO and O01 shouldn't happen, but clearly it's not what I see.

I think p112 implies that the [pairs] entries will look for parameters in 
[atomtypes], complain and use zeroes if lacking, and then apply fudges.

You could compare the results with [pairs] parameters explicitly set to zeroes.

Mark
  
> Yet I checked the manual, page 112 in particular.> 
> It is the first time I come across an example where I have 2 atom in 1-4 
> interaction with such a large opposite charges.  > 
> Is the behaviour I see OK, although apparently rare?> 
> Many thanks in advance,> 
> Alan
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>   Department of Biochemistry, University of Cambridge. 
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
  > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 84 (anisotropic pressure coupling)

Shuangxing Dai wrote:

Well, the final average pressure is not correct:

* **<==  ###  ==>*
* **<  A V E R A G E S  >*
* **<==  ###  ==>*
*
*
*   Energies (kJ/mol)*
*  Buck.ham (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic 
En.*
*1.60633e+06   -5.69243e+06   -3.45003e+06   -7.53612e+06   
 1.80719e+04*

*   Total EnergyTemperature Pressure (bar)*
*   -7.51805e+063.62347e+021.11758e+04*
*
*
*
*
*   Pressure (bar)*
*1.21051e+04   -2.94017e-011.30456e+00*
*   -2.94017e-019.03597e+03   -8.10850e-01*
*1.30456e+00   -8.10850e-011.23863e+04*
*
*
*
*
* **<==  ###  ==>*
* **<  R M S - F L U C T U A T I O N S  >*
* **<==  ###  ==>*
*
*
*   Energies (kJ/mol)*
*  Buck.ham (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic 
En.*
*3.92376e+054.00326e+054.71365e+013.02978e+04   
 2.35039e+03*

*   Total EnergyTemperature Pressure (bar)*
*3.01091e+044.71259e+011.71117e+05*
*
*
*
*
*   Pressure (bar)*
*1.82323e+054.91513e+023.07107e+02*
*4.91513e+022.02402e+053.13857e+02*
*3.07107e+023.13857e+021.30179e+05*
*
*
*Also the fluctuation is very large. I think 200ps is long enough. But 
still I cannot find the equilibrium.*

Then 200 ps is clearly not enough, or your entire procedure is not correct. 
Note too that your temperature (362 K) is not at all close to what you want (300 
K).  You may be setting tau_t incorrectly; check the archives.  This value, when 
using the sd integrator, is not the same as the normal interpretation of 
relaxation time, so instead of 0.1, you may want 1.0 or larger.

*I do not know whether the parameters are wrong or I ran the anisotropic 
pressure coupling wrong. Is *Parrinello-Rahman pressure coupling 
sensitive to the initial pressure? I mean if the initial pressure ( in 
order of GPa), object pressure is 1 bar ( 1e5 Pa). 

If your system is far from equilibrium, it may be beneficial to relax it with a 
weak coupling method (i.e., Berendsen) first.  Otherwise, a system that is not 
close to equilibrium may oscillate very wildly and not converge to the desired 
value.

-Justin

*
*
Thanks,
Shuangxing Dai

On Mon, Jun 14, 2010 at 8:50 PM, > wrote:

Message: 3
Date: Mon, 14 Jun 2010 19:18:14 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] anisotropic pressure coupling
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4c16b8b6.4010...@vt.edu >
Content-Type: text/plain; charset=UTF-8; format=flowed

Shuangxing Dai wrote:
 > Hi all:
 > I was using Parrinello-Rahman for pressure coupling and here
is the
 > mdp file:
 >
 > ; RUN CONTROL PARAMETERS =
 > integrator   = sd
 > ; start time and timestep in ps =
 > tinit= 0
 > dt   = 0.001
 > nsteps   = 20
 > ; number of steps for center of mass motion removal =
 > nstcomm  = 100
 > ; NEIGHBORSEARCHING PARAMETERS =
 > ; nblist update frequency =
 > nstlist  = 50
 > ; ns algorithm (simple or grid) =
 > ns_type  = grid
 >
 > ;OPTIONS FOR PRESSURE COUPLING
 > Pcoupl   = Parrinello-Rahman
 > pcoupltype   = anisotropic
 > tau_p= 1
 > compressibility  = 2.1645e-09  2.1645e-09 2.7322e-09 0 0 0
 > ref_p= 1 1 1 0 0 0
 > ;OPTIONS FOR TEMPERATURE COUPLING
 > tc_grps  = system
 > tau_t= 0.1
 > ref_t= 300
 > ; OPTIONS FOR BONDS =
 > constraints  = hbonds
 > ; Type of constraint algorithm =
 > constraint-algorithm = Lincs
 > ; Do not constrain the start configuration =
 > unconstrained-start  = no
 > ; Relative tolerance of shake =
 > shake-tol= 0.0001
 > ; Highest order in the expansion of the constraint coupling matrix =
 > lincs-order  = 12
 > ; Lincs will write a warning to the stderr if in one step a bond =
 > ; rotates over more degrees than =
 > lincs-warnangle  = 30
 > ; Periodic boundary conditions: xyz, no, xy
 > pbc  = xyz
 > periodic_molecules   = no
 > ; nblist cut-off
 > rlist= 1
 >
 > ; OPTIONS FOR ELECTROSTATICS AND VDW
 > ; Method for doing electrostatics
 > coulombtype  = PME
 > rcoulomb = 1
 > ; Method for doing Van der Waals
 > vdw-type = Cut-off
 > ; cut-off lengths
 > rvdw = 1
 >
 > ; Spacing f

Re: [gmx-users] Positive Total energy



- Original Message -
From: Thanasis Koukoulas 
Date: Tuesday, June 15, 2010 4:55
Subject: [gmx-users] Positive Total energy
To: gmx-users@gromacs.org

---
| > Hello 
> I have sent several emails and i am sorry. It is my last attempt to finish 
> this simulation.> The molecule i have is C-C-C-C-C-C-O-C-C-O-C-C-O-H or 
> C10H1O3. (ciej molecule)> 
> I dont use gromacs libraries> the files i use are attached to the email in 
> which i have descriped step by step the forcefield i use. > as you can see in 
> [pairs] i have an extra non Lj 1-4 pair. i did it because the model i use has 
> a potential between atom 10 and 14 ether oxygen and alchohol hydrogen 
> interaction. It is described in the paper as a repulsive energy between these 
> two atoms. and it has a formula:> 
> Erepulsive = 3.325789e-7/r^12> 
> the only way to import in gromacs i think is this:> 
> [ pairs ]> ; ai aj  funct > 10 142 0 0 0 0 3.325789e-7> 
> it is an intra-molecular only interaction. so i couldnt think another way to 
> do it except this. as you can see i have several zeros for the charges, C6=o 
> and C12 = 3.325789e-7 fidgeQQ=0 for this case> 
> the problem is i get positive total energy. i did this sim for only one 
> molecule just to see what is wrong and i think that coulomb (SR) are wrong 
> for sure.> 
> so i want > 
> coulomb 1-4 /2   !thats why i put fudgeQQ = 0.5> 
> the values i get at the step 0 are> 
> Energies (kJ/mol)>   AngleProper Dih.  LJ-14 
> Coulomb-14LJ (SR)> 2.30340e+031.08417e+00 3.16570e+00
> 8.79204e+04   -2.54164e+03>   Disper. corr.   Coulomb (SR)   Coul. recip. 
>  PotentialKinetic En.>-2.51250e+00   -4.81042e+04   -2.84931e+04
> 1.10867e+041.84852e+04>Total EnergyTemperature Pressure (bar)  
> Cons. rmsd ()> 2.95719e+042.99528e+02   -3.03583e+023.13477e-06

 |
---
OK, now that you've simplified, it seems reasonably clear that Coulomb-14 is 
badly broken. My leading theory is that grompp is somehow reading (part of) the 
text of your C12 value into a charge field.

I would test with this [pairs] line commented out, with zero in place of your 
intended C12 value, and with your C12 value expressed as 0.0325789. If that 
doesn't shed light on the nature of the problem, please report the Step 0 
energies (as above) in each case.

Then, use

gmxdump -s topol.tpr | less

and search for 3.257 and maybe attach 50 lines either side of the line that 
looks like it matches that value in a parameter entry. Don't attach the whole 
file, it'll be huge.

As a side point, the contents of your #included files seems to achieve a 
correct result, although your organization of the content with respect to the 
filenames is badly at odds with the correct approach, and will give you 
problems later. Compare with a simple tutorial example.

Mark

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] sc_power

2010-06-14 Thread fancy2012

Hi GMX users,
What is the difference between the values of sc_power, 1 and 2? Thanks very 
much!
 
All the best,
fancy-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths

I used the same commands trying another proteins, but no problems. So it's not 
the reason about the commands I used.

It did not contain the same number of molecules after genion when I changed the 
box size. The pressure coupling was not on, and I did not reach this steps. The 
problem I had just the steps I did the energy minimization after ions (NA+ and 
CL-) added. 

Thanks and regards,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 6:48 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

Please copy and paste in the commands you are using, and the output.

I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupling on. So when you
start the simulation, not surprising that the box compresses again and
goes under 2nm again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 12:04 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Monday, June 14, 2010 10:02 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] the box lengths
>
> #ZHAO LINA# wrote:
> > ___
> > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
> on behalf of Justin A. Lemkul [jalem...@vt.edu]
> > Sent: Monday, June 14, 2010 9:33 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] the box lengths
> >
> > #ZHAO LINA# wrote:
> >>  Hi,
> >>
> >> First time I meet this problem,
> >> ERROR: One of the box lengths is smaller than twice the cut-off
> length.
> >> Increase the box size or decrease rlist.
> >> I just followed the advice increase the box size, I tried twice in
> the
> >> editconf about the box size, actually this box is really large
> enough
> >> for the testing consideration, but still has the same problem.
> >>
> >
> > Well, what are your box vectors?  If they are < 2 nm, you will get
> this error
> > because of the minimum image convention.
> >
> >
>
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
> on
> >
> > -Justin
> >
> > system size :  4.581  2.380  2.715 (nm)
> > diameter:  4.889   (nm)
> > center  : -0.012  0.003 -0.904 (nm)
> > box vectors :  0.000  0.000  0.000 (nm)
> > box angles  :   0.00   0.00   0.00 (degrees)
> > box volume  :   0.00   (nm^3)
> > shift   :  9.678  9.664  5.461 (nm)
> > new center  :  9.667  9.667  4.557 (nm)
> > new box vectors : 12.889 12.889 12.889 (nm)
> > new box angles  :  60.00  60.00  90.00 (degrees)
> > new box volume  :1514.05   (nm^3)
> >
> > This one I set was really large, but still showed that problems.
> >
>
> What problems?  The same error about the box lengths being shorter
than
> twice
> the cutoff?  I don't think that's possible, given those vectors, if
> you're
> keeping your cutoffs at 1.0 nm.
>
> -Justin
>
> I do keep the cut-off. That's I do not know why. Four times had been
> tried.
>
> > Thanks,
> >
> > lina
> >
> >
> >
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/m

Re: [gmx-users] sc_power



- Original Message -
From: fancy2012 
Date: Tuesday, June 15, 2010 12:28
Subject: [gmx-users] sc_power
To: gmx-users 

> Hi GMX users, > What is the difference between the values of sc_power, 1 and 
> 2? Thanks very much!

What is written in section 4.5.1 of the manual?

Mark

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] the box lengths




#ZHAO LINA# wrote:

I used the same commands trying another proteins, but no problems. So it's not 
the reason about the commands I used.



The problem is not whether or not your commands work for other systems, rather 
the fact that they are (for some reason) not working for this particular system. 
 Most standard commands work just fine.  The reason I asked originally was to 
see exactly what your commands were to check if you were using the right files 
instead of accidentally repeating the commands on the coordinate file with the 
improper box vectors.


That is also (I suspect) the reason Dallas asked for you to copy and paste all 
your commands.


We can't get inside your head to see what you're doing, so if you want free 
help, you need to provide the information we ask for so we can quickly resolve 
this.  If grompp is still complaining about box vectors, you're either using the 
wrong coordinate file, or you've somehow managed to mangle the coordinate file 
format.  Without seeing your actual commands and any other relevant details, the 
best anyone can offer is "you're doing something wrong."


-Justin

It did not contain the same number of molecules after genion when I changed the box size. The pressure coupling was not on, and I did not reach this steps. The problem I had just the steps I did the energy minimization after ions (NA+ and CL-) added. 


Thanks and regards,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 6:48 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

Please copy and paste in the commands you are using, and the output.

I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupling on. So when you
start the simulation, not surprising that the box compresses again and
goes under 2nm again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.



-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 15 June 2010 12:04 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]

on behalf of Justin A. Lemkul [jalem...@vt.edu]

Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:

 Hi,

First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off

length.

Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in

the

editconf about the box size, actually this box is really large

enough

for the testing consideration, but still has the same problem.


Well, what are your box vectors?  If they are < 2 nm, you will get

this error

because of the minimum image convention.



http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi

on

-Justin

system size :  4.581  2.380  2.715 (nm)
diameter:  4.889   (nm)
center  : -0.012  0.003 -0.904 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  9.678  9.664  5.461 (nm)
new center  :  9.667  9.667  4.557 (nm)
new box vectors : 12.889 12.889 12.889 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1514.05   (nm^3)

This one I set was really large, but still showed that problems.


What problems?  The same error about the box lengths being shorter

than

twice
the cutoff?  I don't think that's possible, given those vectors, if
you're
keeping your cutoffs at 1.0 nm.

-Justin

I do keep the cut-off. That's I do not know why. Four times had been
tried.


Thanks,

lina




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.

Re: RE: [gmx-users] the box lengths



- Original Message -
From: #ZHAO LINA# 
Date: Tuesday, June 15, 2010 12:34
Subject: RE: [gmx-users] the box lengths
To: Discussion list for GROMACS users 

> I used the same commands trying another proteins, but no 
> problems. So it's not the reason about the commands I used.

Whether the commands work on some presumably-larger system is not the issue. 
The way the contents of your *small* system interact with your commands is the 
issue. You are describing anomalous behaviour. That's probably because you're 
doing something wrong, so we want to see your actual command lines and output 
to help you learn why this is happening. Accordingly, we're not all that 
interested in things that have been filtered through your head :-) If the 
current knowledge in your head was accurate, you wouldn't be needing help :-)

Mark

> 
> It did not contain the same number of molecules after genion 
> when I changed the box size. The pressure coupling was not on, 
> and I did not reach this steps. The problem I had just the steps 
> I did the energy minimization after ions (NA+ and CL-) added. 
> 
> Thanks and regards,
> 
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-
> boun...@gromacs.org] on behalf of Dallas B. Warren 
> [dallas.war...@pharm.monash.edu.au]sent: Tuesday, June 15, 2010 
> 6:48 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> Please copy and paste in the commands you are using, and the output.
> 
> I suspect you have made your box bigger, but it still contains 
> the same
> number of molecules and you still have pressure coupling on. So 
> when you
> start the simulation, not surprising that the box compresses 
> again and
> goes under 2nm again.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> -
> When the only tool you own is a hammer, every problem begins to 
> resemblea nail.
> 
> 
> > -Original Message-
> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> > Sent: Tuesday, 15 June 2010 12:04 AM
> > To: jalem...@vt.edu; Discussion list for GROMACS users
> > Subject: RE: [gmx-users] the box lengths
> >
> >
> > 
> > From: gmx-users-boun...@gromacs.org [gmx-users-
> boun...@gromacs.org] on
> > behalf of Justin A. Lemkul [jalem...@vt.edu]
> > Sent: Monday, June 14, 2010 10:02 PM
> > To: Gromacs Users' List
> > Subject: Re: [gmx-users] the box lengths
> >
> > #ZHAO LINA# wrote:
> > > ___
> > > From: gmx-users-boun...@gromacs.org [gmx-users-
> boun...@gromacs.org]> on behalf of Justin A. Lemkul [jalem...@vt.edu]
> > > Sent: Monday, June 14, 2010 9:33 PM
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] the box lengths
> > >
> > > #ZHAO LINA# wrote:
> > >>  Hi,
> > >>
> > >> First time I meet this problem,
> > >> ERROR: One of the box lengths is smaller than twice the cut-off
> > length.
> > >> Increase the box size or decrease rlist.
> > >> I just followed the advice increase the box size, I tried 
> twice in
> > the
> > >> editconf about the box size, actually this box is really large
> > enough
> > >> for the testing consideration, but still has the same problem.
> > >>
> > >
> > > Well, what are your box vectors?  If they are < 2 
> nm, you will get
> > this error
> > > because of the minimum image convention.
> > >
> > >
> >
> http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
> > on
> > >
> > > -Justin
> > >
> > > system size :  4.581  
> 2.380  2.715 (nm)
> > > diameter:  
> 4.889   (nm)
> > > center  
> : -0.012  0.003 -0.904 (nm)
> > > box vectors :  0.000  
> 0.000  0.000 (nm)
> > > box angles  :   
> 0.00   0.00   0.00 (degrees)
> > > box volume  :   
> 0.00   (nm^3)
> > > 
> shift   :  9.678  
> 9.664  5.461 (nm)
> > > new center  :  9.667  
> 9.667  4.557 (nm)
> > > new box vectors : 12.889 12.889 12.889 (nm)
> > > new box angles  :  60.00  60.00  90.00 
> (degrees)> > new box volume  
> :1514.05   (nm^3)
> > >
> > > This one I set was really large, but still showed that problems.
> > >
> >
> > What problems?  The same error about the box lengths 
> being shorter
> than
> > twice
> > the cutoff?  I don't think that's possible, given those 
> vectors, if
> > you're
> > keeping your cutoffs at 1.0 nm.
> >
> > -Justin
> >
> > I do keep the cut-off. That's I do not know why. Four times 
> had been
> > tried.
> >
> > > Thanks,
> > >
> > > lina
> > >
> > >
> > >
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Depa

RE: [gmx-users] the box lengths

As already mentioned by Justin, unless you copy and paste the commands
and output you got, for us to see, we can only have stabs in the dark
(which is what I did since you are missing lots of information on what
you are actually doing) to what is actually going on.  And don't type in
the commands into your email client, physically go and copy and paste
the text in, otherwise you are filtering it through your own mind.

Go and run the series of commands that work, copy / paste the results
for us to see.

Then go and run the series of commands that don't work, copy / paste
again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 12:32 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> I used the same commands trying another proteins, but no problems. So
> it's not the reason about the commands I used.
> 
> It did not contain the same number of molecules after genion when I
> changed the box size. The pressure coupling was not on, and I did not
> reach this steps. The problem I had just the steps I did the energy
> minimization after ions (NA+ and CL-) added.
> 
> Thanks and regards,
> 
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
> Sent: Tuesday, June 15, 2010 6:48 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> Please copy and paste in the commands you are using, and the output.
> 
> I suspect you have made your box bigger, but it still contains the
same
> number of molecules and you still have pressure coupling on. So when
> you
> start the simulation, not surprising that the box compresses again and
> goes under 2nm again.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> -
> When the only tool you own is a hammer, every problem begins to
> resemble
> a nail.
> 
> 
> > -Original Message-
> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> > Sent: Tuesday, 15 June 2010 12:04 AM
> > To: jalem...@vt.edu; Discussion list for GROMACS users
> > Subject: RE: [gmx-users] the box lengths
> >
> >
> > 
> > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
> on
> > behalf of Justin A. Lemkul [jalem...@vt.edu]
> > Sent: Monday, June 14, 2010 10:02 PM
> > To: Gromacs Users' List
> > Subject: Re: [gmx-users] the box lengths
> >
> > #ZHAO LINA# wrote:
> > > ___
> > > From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org]
> > on behalf of Justin A. Lemkul [jalem...@vt.edu]
> > > Sent: Monday, June 14, 2010 9:33 PM
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] the box lengths
> > >
> > > #ZHAO LINA# wrote:
> > >>  Hi,
> > >>
> > >> First time I meet this problem,
> > >> ERROR: One of the box lengths is smaller than twice the cut-off
> > length.
> > >> Increase the box size or decrease rlist.
> > >> I just followed the advice increase the box size, I tried twice
in
> > the
> > >> editconf about the box size, actually this box is really large
> > enough
> > >> for the testing consideration, but still has the same problem.
> > >>
> > >
> > > Well, what are your box vectors?  If they are < 2 nm, you will get
> > this error
> > > because of the minimum image convention.
> > >
> > >
> >
>
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
> > on
> > >
> > > -Justin
> > >
> > > system size :  4.581  2.380  2.715 (nm)
> > > diameter:  4.889   (nm)
> > > center  : -0.012  0.003 -0.904 (nm)
> > > box vectors :  0.000  0.000  0.000 (nm)
> > > box angles  :   0.00   0.00   0.00 (degrees)
> > > box volume  :   0.00   (nm^3)
> > > shift   :  9.678  9.664  5.461 (nm)
> > > new center  :  9.667  9.667  4.557 (nm)
> > > new box vectors : 12.889 12.889 12.889 (nm)
> > > new box angles  :  60.00  60.00  90.00 (degrees)
> > > new box volume  :1514.05   (nm^3)
> > >
> > > This one I set was really large, but still showed that problems.
> > >
> >
> > What problems?  The same error about the box lengths being shorter
> than
> > twice
> > the cutoff?  I don't think

RE: [gmx-users] the box lengths

Hi,

That's very nice all of you. I was just worried that so many details would make 
things blur.


pdb2gmx -f try2.pdb -o try2.gro -ignh 

then choose ffG53a6,

below is the minim.mdp going to be used (more than once).
//
; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator  = steep 
emtol   = 1.0   
nsteps  = 500   
nstenergy   = 1 
energygrps  = System

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
ns_type = simple
coulombtype = cut-off
rcoulomb= 1.0   
rvdw= 1.0   
constraints = none  
pbc = no
///

grompp  -f minim.mdp -c try2.gro -p topol.top -o try2-vacuum.tpr
mdrun -deffnm try2-vacuum -c try2-vacuum.pdb

below is the mdrun results:
///
Reading file try2-vacuum.tpr, VERSION 4.0.7 (single precision)
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps=  500

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 190 steps,
but did not reach the requested Fmax < 1.
Potential Energy  = -9.8216992e+02
Maximum force =  2.7798114e+02 on atom 334
Norm of force =  5.9967701e+01
/

editconf -f try2-vacuum.pdb -o try2-newbox.gro -bt dodecahedron -d 2.0

(P.S I used the -d 4.0 once, just a bit crazy large to test it)
/

No velocities found
system size :  4.567  2.350  1.422 (nm)
diameter:  4.619   (nm)
center  : -0.010 -0.047 -0.232 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  6.474  6.511  3.279 (nm)
new center  :  6.464  6.464  3.047 (nm)
new box vectors :  8.619  8.619  8.619 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 452.68   (nm^3)
/

genbox -cp try2-newbox.gro -cs spc216.gro -p topol.top -o try2-water.pdb


Containing 450 atoms in 52 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 5x5x4 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL (   3 atoms): 21600 residues
Calculating Overlap...
box_margin = 0.315
Removed 14442 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Grid: 21 x 21 x 15 cells
Succesfully made neighbourlist
nri = 89426, nrj = 2521641
Checking Protein-Solvent overlap: tested 8637 pairs, removed 783 atoms.
Checking Solvent-Solvent overlap: tested 474780 pairs, removed 5133 atoms.
Added 14814 molecules
Generated solvent containing 2 atoms in 14814 residues
Writing generated configuration to try2-water.pdb
Protein

Output configuration contains 44892 atoms in 14866 residues
Volume : 452.675 (nm^3)
Density: 999.711 (g/l)
Number of SOL molecules:  14814   

Processing topology
Adding line for 14814 solvent molecules to topology file (topol.top)

//


grompp  -f minim.mdp -c try2-water.pdb -p topol.top -o try2-water.tpr

genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ 
-nname CL-

/
Reading file try2-water.tpr, VERSION 4.0.7 (single precision)
Using a coulomb

Re: [gmx-users] the box lengths

2010-06-14 Thread Tsjerk Wassenaar

Hi,

Which version of gromacs was this again? There have been issues with
pdb files being written without box (CRYST1) records, recorded in the
archive. Check the output .pdb files, especially after calling genbox
(grep "^CRYST1" file.pdb). Also, try the sequence always writing .gro
files as output.

Hope it helps,

Tsjerk

On Tue, Jun 15, 2010 at 6:12 AM, #ZHAO LINA#  wrote:
> Hi,
>
> That's very nice all of you. I was just worried that so many details would 
> make things blur.
>
>
> pdb2gmx -f try2.pdb -o try2.gro -ignh
>
> then choose ffG53a6,
>
> below is the minim.mdp going to be used (more than once).
> //
> ; Define can be used to control processes
> define          = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep
> emtol           = 1.0
> nsteps          = 500
> nstenergy       = 1
> energygrps      = System
>
> ; Parameters describing how to find the neighbors of each atom and how to 
> calculate the interactions
> ns_type         = simple
> coulombtype     = cut-off
> rcoulomb        = 1.0
> rvdw            = 1.0
> constraints     = none
> pbc             = no
> ///
>
> grompp  -f minim.mdp -c try2.gro -p topol.top -o try2-vacuum.tpr
> mdrun -deffnm try2-vacuum -c try2-vacuum.pdb
>
> below is the mdrun results:
> ///
> Reading file try2-vacuum.tpr, VERSION 4.0.7 (single precision)
> Steepest Descents:
>   Tolerance (Fmax)   =  1.0e+00
>   Number of steps    =          500
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1
>
> Double precision normally gives you higher accuracy.
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 190 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy  = -9.8216992e+02
> Maximum force     =  2.7798114e+02 on atom 334
> Norm of force     =  5.9967701e+01
> /
>
> editconf -f try2-vacuum.pdb -o try2-newbox.gro -bt dodecahedron -d 2.0
>
> (P.S I used the -d 4.0 once, just a bit crazy large to test it)
> /
>
> No velocities found
>    system size :  4.567  2.350  1.422 (nm)
>    diameter    :  4.619               (nm)
>    center      : -0.010 -0.047 -0.232 (nm)
>    box vectors :  0.000  0.000  0.000 (nm)
>    box angles  :   0.00   0.00   0.00 (degrees)
>    box volume  :   0.00               (nm^3)
>    shift       :  6.474  6.511  3.279 (nm)
> new center      :  6.464  6.464  3.047 (nm)
> new box vectors :  8.619  8.619  8.619 (nm)
> new box angles  :  60.00  60.00  90.00 (degrees)
> new box volume  : 452.68               (nm^3)
> /
>
> genbox -cp try2-newbox.gro -cs spc216.gro -p topol.top -o try2-water.pdb
>
> 
> Containing 450 atoms in 52 residues
> Initialising van der waals distances...
> Reading solvent configuration
> "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
> solvent configuration contains 648 atoms in 216 residues
>
> Initialising van der waals distances...
> Will generate new solvent configuration of 5x5x4 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
>    SOL (   3 atoms): 21600 residues
> Calculating Overlap...
> box_margin = 0.315
> Removed 14442 atoms that were outside the box
> Neighborsearching with a cut-off of 0.48
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
> System total charge: 0.000
> Grid: 21 x 21 x 15 cells
> Succesfully made neighbourlist
> nri = 89426, nrj = 2521641
> Checking Protein-Solvent overlap: tested 8637 pairs, removed 783 atoms.
> Checking Solvent-Solvent overlap: tested 474780 pairs, removed 5133 atoms.
> Added 14814 molecules
> Generated solvent containing 2 atoms in 14814 residues
> Writing generated configuration to try2-water.pdb
> Protein
>
> Output configuration contains 44892 atoms in 14866 residues
> Volume                 :     452.675 (nm^3)
> Density                :     999.711 (g/l)
> Number of SOL molecules:  14814
>
> Processing topology
> Adding line for 14814 solvent molecules to topology file (topol.t

RE: [gmx-users] the box lengths

What is the contents of the CRYST1 line in the file try2-water-ions.pdb?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths

There is none CRYST1 line in the file try2-water-ions.pdb.

Thanks and regards,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 1:24 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

What is the contents of the CRYST1 line in the file try2-water-ions.pdb?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths

Well, there's ya problem :-)

That specifies the box dimensions.

Have a look at try2-water.pdb as well, then you should be able to pin
down where the issue has arisen.  Appears that one of those steps have
failed to write the box dimensions.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> There is none CRYST1 line in the file try2-water-ions.pdb.
> 
> Thanks and regards,
> 
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
> Sent: Tuesday, June 15, 2010 1:24 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> What is the contents of the CRYST1 line in the file try2-water-
> ions.pdb?
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> -
> When the only tool you own is a hammer, every problem begins to
> resemble
> a nail.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths

Well...

There is one line in try2-water.pdb, shows as below

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   86.185   86.185   86.185  60.00  60.00  90.00 P 1   1

Do you think something was wrong during
genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ 
-nname CL-

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 1:41 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

Well, there's ya problem :-)

That specifies the box dimensions.

Have a look at try2-water.pdb as well, then you should be able to pin
down where the issue has arisen.  Appears that one of those steps have
failed to write the box dimensions.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> There is none CRYST1 line in the file try2-water-ions.pdb.
>
> Thanks and regards,
>
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
> Sent: Tuesday, June 15, 2010 1:24 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> What is the contents of the CRYST1 line in the file try2-water-
> ions.pdb?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> -
> When the only tool you own is a hammer, every problem begins to
> resemble
> a nail.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] the box lengths