date:20101201

On 2/12/2010 4:16 PM, WU Yanbin wrote:

Dear GMXers,

I'm running a simulation of water contact angle measurement on top of
graphite surface.
Initially a water cubic box is placed on two-layer graphite surface
with the rest of the box being vacuum. The water droplet is relaxed
during the simulation to develop a spherical shape.

An error of "X particles communicated to PME node Y are more than a
cell length out of the domain decomposition cell of their charge
group" was encountered.

And I have read the suggested solutions at the link below
http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group.

I guess the reason for this error in my case is because of the vacuum
such that the water molecules at the boundary of the droplet can move
fast. I have check the trajectory and the simulation is OK.

I doubt the simulation is OK. This error message is one of several that
can happen when the system is not well-enough conditioned for the MD to
be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up.
Here, you have atoms moving much faster than GROMACS was engineered to
expect.

You should be confident that a water drop in a vacuum, and your graphite
surface are both stable on their own before you try the wetting simulation.

For this situation, is there a way of suppressing this error? Or what
else can I do?

Work out why it's poorly conditioned.

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/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

2010-12-01 Thread WU Yanbin

Dear GMXers,

I'm running a simulation of water contact angle measurement on top of
graphite surface.
Initially a water cubic box is placed on two-layer graphite surface with the
rest of the box being vacuum. The water droplet is relaxed during the
simulation to develop a spherical shape.

An error of "X particles communicated to PME node Y are more than a cell
length out of the domain decomposition cell of their charge group" was
encountered.
And I have read the suggested solutions at the link below
http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
.

I guess the reason for this error in my case is because of the vacuum such
that the water molecules at the boundary of the droplet can move fast. I
have check the trajectory and the simulation is OK.

For this situation, is there a way of suppressing this error? Or what else
can I do?

PS: the GROMACS version I'm using is GROMACS4.5.

Thank you.

Best,
Yanbin
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] Restraining water


On 2/12/2010 12:51 PM, Guido Polles wrote:

Hi,
I know it looks a little bit strange, but i was trying to restrain
just some water in my system.
Now, if i put something like
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
I put restraints on all the molecules.


Yes, that directive will pertain to all the molecules that have that [ 
moleculetype ]. I'm not sure if you only want position restraints on 
some of your water molecules.



I thought about a turnaround,  just making a second water molecule
type, but now complains about using more than one settle type.
Is there any other way to do it?
And if I follow the "Suggestion: change the least use settle
constraints into 3 normal constraints" I have to worry about some kind
of huge loss in performance?


I would expect the non-settle waters to use the solvent-optimized loops 
in the normal way, so there should be no difference in execution time 
between the unrestrained all-settle simulation and the partly-restrained 
party-settled simulation. Obviously, this is straightforward to test.


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/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Re: air-water interface

2010-12-01 Thread Vitaly Chaban

> Hi, everyone
>
> I find that i used T and P coupling in water-air interface, that is the 
> reason my system imploded.
>
> So i changed to NVT. But there are still fatal errors.
>
> I have some questions concerning  .gro file.
>
> for example in spc216.gro, there are both + and - psotions. But in other .gro 
> file, all is + postion.
>
> What is the difference between .gro ?


No difference since PBC works.


Dr. Vitaly V. 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/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Restraining water

2010-12-01 Thread Guido Polles

Hi,
I know it looks a little bit strange, but i was trying to restrain
just some water in my system.
Now, if i put something like
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
I put restraints on all the molecules.
I thought about a turnaround,  just making a second water molecule
type, but now complains about using more than one settle type.
Is there any other way to do it?
And if I follow the "Suggestion: change the least use settle
constraints into 3 normal constraints" I have to worry about some kind
of huge loss in performance?
Thank you

Guido
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] RE:C6 attractive term off OPLSAA


On 2/12/2010 7:40 AM, nishap.pa...@utoronto.ca wrote:
Would I change the sigma to negative in my nb.itp file the way it is 
set or do I need to include a [nonbond_params] section and make sigma 
negative in that specific section? because I realize from the manual 
OPLS-AA uses combination rule 3 but in the manual it shows to combine 
sigma for i and j using rule 2 and rule 1 and 3 correspond to C6 and 
C12 for i and j. Is that correct?


This is too convoluted for me to understand :-)

Mark



Quoting nishap.pa...@utoronto.ca:


I am going to give that a try. Thanks.


Quoting Berk Hess :



Hi,

Maybe it is not so clear from the topology table in the manual, but 
  when you supply
sigma and epsilon as non-bonded parameters, as for OPLS, the 
nonbond_params

section also expects sigma and epsilon.
So it seems you could not set only C6 to zero.
However there is an, undocumented, trick: if you use a negative sigma,
C6 is set to zero.

Berk


Date: Wed, 1 Dec 2010 10:42:11 -0500
From: nishap.pa...@utoronto.ca
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] C6 attractive term off OPLSAA

I see. I actually want to compare my RDFs with C6 term off. Earlier I
tried using force.c code file and turned C6 = 0, but when i compared
my RDFs, it didn't look any different so I am not sure if it even
worked at all or made any difference to the simulation, but again I
was using OPLS-AA and the nb.itp file itself does not indicate value
for C6 or C12.

If there any other way I could achieve this?



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

I ran the simulation using a different force field ffG53a6. I
modified the ffG53a6nb.itp file by changing the term C6 to zero for
 nonbonded parameters, but this time for urea in water. The
simulation ran fine without any warning or exploding. I don't
understand why it would work with one force-field and not with
OPLS-AA.



I don't understand why it worked at all, frankly, but more than 
likely
you've been lucky enough to make 53a6 work, but OPLS-AA failed.  
You're

making significant alterations to the nonbonded interactions of the
system.


Also using mdrun -rerun, I would basically use the nb.itp file with
 nonbonded parameters as mentioned earlier and everything else is
the same i.e. my .mdp parameters and do another run using my
previous trajectory file? I tried to look through some of the posts
 for using -rerun but I don't understand how that would not still
blow up the system. I would like to give it a try for sure but I am
 not quite sure how I would use the command as such.



Using mdrun -rerun recalculates energies from an existing trajectory.
You would generate a trajectory with a normal force field model, then
create a new .tpr file that has your modified potential, such that 
you

can decompose the energy terms cleverly.  If your goal is to generate
trajectories to study the effects of using a modified potential 
(i.e.,

C6 = 0), then you can't use -rerun.

-Justin


I really appreciate the help.

Thanks.


Quoting Mark Abraham :


On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:



nishap.pa...@utoronto.ca wrote:

I tried using the nonbonded parameters as defined below in my
ffoplsaanb.itp file for methanol in water and this is the syntax
 I  used:

[nonbond_params]
;ijfuncc6c12
opls_154opls_11110.00E+0002.43E-006
opls_154opls_11210.00E+0000.00E+000
opls_154opls_112  10.00E+0000.00E+000
opls_155opls_111  10.00E+0000.00E+000
opls_155opls_112  10.00E+0000.00E+000
opls_155opls_112  10.00E+0000.00E+000
opls_156opls_111  10.00E+0002.70E-007
opls_156opls_112  10.00E+0000.00E+000
opls_156opls_11210.00E+0000.00E+000
opls_157opls_111  10.00E+0003.01E-006
opls_157opls_112  10.00E+0000.00E+000

When I tried to do mdrun, I got an error saying my system is
exploding. I tried doing the mdrun without nonbonded parameters
 and it runs fine. So I am not sure if I am using the
nonbond_params concept correctly. i.e. I want C6 to be zero
between my solute (methanol) and solvent (water). This is the
error:

Warning: 1-4 interaction between 2 and 6 at distance 3.786 which
  is larger than the 1-4 table size 2.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Suggestions?



Your implementation of your concept is technically correct, but
perhaps physically unreasonable.  You're turning off the
attractive  LJ component and leaving only a repulsive component.
 It sounds  about right that everything is flying apart.


Indeed. The way to do this is with mdrun -rerun on a trajectory
generated with the normal version of the forcefield, as I think 
I said

in another thread yesterday.

Mark



-Justin


Thanks.

-Nisha P

Quoting nishap.pa...@utoronto.ca:

Oka

Re: [gmx-users] virtual sites and heavy atoms for longer time steps


On 2/12/2010 11:13 AM, Hassan Shallal wrote:

I have some issues to discuss with the mailing list users,

1- Is using virtual sites alone enough to allow me to lengthen the time step 
from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology 
files in order to use 4 fs time step?

2- Another question, does vitual sites (assigning virtual hydrogens a mass of 
zero and adding their masses to the connected heavy atoms) opposes the effect 
of heavy atoms (increases the mass of the hydroen atoms) or vice versa.
Or is the situation that heavy atoms treatment applies  when virtual sites 
treatment is not implemented, and we end up with a systme where some hydrogen 
atoms have no masses at all (those as virtual sites) whereas other hydrogen 
atoms are much heavier (those treated as heavy hydrogens)?

3- Implementing the scenario of some hydrogen atoms having zero masses and 
others having heavier masses, how would that affect the accuracy of predicting 
some energetic aspects like H-bonding? I know there is always a trade between 
efficiency or fastness and the accuracy because approximations usually fasten 
the job while decreasing the accuracy, but from experienced users point of 
view, how dangerous that approximation would be?

Any answers or clarification of the above issues will be so much appreciated


Perhaps manual section 6.5 and ref therein will clarify some of this.

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/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] virtual sites and heavy atoms for longer time steps

2010-12-01 Thread Hassan Shallal

I have some issues to discuss with the mailing list users,
 
1- Is using virtual sites alone enough to allow me to lengthen the time step 
from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology 
files in order to use 4 fs time step?
 
2- Another question, does vitual sites (assigning virtual hydrogens a mass of 
zero and adding their masses to the connected heavy atoms) opposes the effect 
of heavy atoms (increases the mass of the hydroen atoms) or vice versa. 
Or is the situation that heavy atoms treatment applies  when virtual sites 
treatment is not implemented, and we end up with a systme where some hydrogen 
atoms have no masses at all (those as virtual sites) whereas other hydrogen 
atoms are much heavier (those treated as heavy hydrogens)?
 
3- Implementing the scenario of some hydrogen atoms having zero masses and 
others having heavier masses, how would that affect the accuracy of predicting 
some energetic aspects like H-bonding? I know there is always a trade between 
efficiency or fastness and the accuracy because approximations usually fasten 
the job while decreasing the accuracy, but from experienced users point of 
view, how dangerous that approximation would be?
 
Any answers or clarification of the above issues will be so much appreciated
 
Hassan



From: gmx-users-boun...@gromacs.org on behalf of Roland Schulz
Sent: Wed 12/1/2010 2:15 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Cut-offs using CHARMM27 ff




On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal  wrote:


Dear Gromacs users,
 
I am trying to use CHARMM27 taking the simulation conditions of two 
recent articles as guides in optimizing the simulation parameters. (DOI: 
10.1021/ct900549r and DOI: 10.1021/jp101581h). 
 
-- Both are using PME for electrostatics and I am planning to do that 
too
-- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force 
field as mentioned)
-- In the second paper, they have explicitly assigned rvdw = 1.2 (this 
value is also optimized for CHARMM27 force field) and they assigned the NS 
rlist = 1.2 because as I understand, using PME as a coulombtype requires 
rcoulomb to be equal to rlist. I have no problem following up until now and it 
seems that (rlist = rcoulomb = rvdw = 1.2) presents the best combination of 
cut-offs for using (coulombtype = PME and vdwtype = cut-off) along with CHARMM27
 
-- What I can't get is that in the first paper, they mentioned the 
following "van der Waals interactions were switched off between 1.0 to 1.2 nm"
what does that mean in terms of cut-offs and vdwtype?
Does that mean vdwtype = switch, vdw_switch = 1, rvdw = 1.2 ? 

yes. 


and if this is what is meant, then rlist has to be 0.1-0.3 larger than 
rvdw to accomodate for the size of the charge groups as mentioned in the manual 
and accordingly, we can't keep rcoulomb = 1.2 because rcoulomb must be equal to 
rlist to allow using PME.

CHARMM FF doesn't use charge groups. Thus (as far as I understand) this warning 
can be ignored.  You still miss a few interactions because the neighbor-list 
only contains everything up to 1.2 thus an atom at a distance just above 1.2 
and moves a bit inwards, it is not included until the next neighbor-list 
update. But because the interaction is already switched it is not very critical 
in my opinion. If you want to avoid this you can use PME-Switch but this is 
significant slower.

Roland 


 
 
 

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists





-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov  
865-241-1537, ORNL PO BOX 2008 MS6309

<>-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] Cut-offs using CHARMM27 ff

2010-12-01 Thread Roland Schulz

On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal  wrote:

>  Dear Gromacs users,
>
> I am trying to use CHARMM27 taking the simulation conditions of two recent
> articles as guides in optimizing the simulation parameters. *(DOI: 
> *10.1021/ct900549r
> and *DOI:* 10.1021/jp101581h).
>
> -- Both are using PME for electrostatics and I am planning to do that too
> -- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force field
> as mentioned)
> -- In the second paper, they have explicitly assigned rvdw = 1.2
> (this value is also optimized for CHARMM27 force field) and they assigned
> the NS rlist = 1.2 because as I understand, using PME as a coulombtype
> requires rcoulomb to be equal to rlist. I have no problem following up
> until now and it seems that (rlist = rcoulomb = rvdw = 1.2) presents the
> best combination of cut-offs for using (coulombtype = PME and vdwtype =
> cut-off) along with CHARMM27
>
> -- What I can't get is that in the first paper, they mentioned the
> following *"van der Waals interactions were switched off between 1.0 to
> 1.2 nm"*
> *what does that mean in terms of cut-offs and vdwtype?*
> Does that mean *vdwtype = switch*, *vdw_switch* *= 1*, *rvdw = 1.2* ?
>
yes.

> and if this is what is meant, then rlist has to be 0.1-0.3 larger than rvdw
> to accomodate for the size of the charge groups as mentioned in the manual
> and accordingly, we can't keep rcoulomb = 1.2 because rcoulomb must be equal
> to rlist to allow using PME.
>
CHARMM FF doesn't use charge groups. Thus (as far as I understand) this
warning can be ignored.  You still miss a few interactions because
the neighbor-list only contains everything up to 1.2 thus an atom at a
distance just above 1.2 and moves a bit inwards, it is not included until
the next neighbor-list update. But because the interaction is already
switched it is not very critical in my opinion. If you want to avoid this
you can use PME-Switch but this is significant slower.

Roland

>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero

2010-12-01 Thread Roland Schulz

Hi,

you can use trjconv to write frames to GRO format. Or you can use it to
write a trajectory from a different starting point (and then you can use
gmxdump).

Roland

On Wed, Dec 1, 2010 at 4:39 PM, Silvia Crivelli wrote:

> Hello,
>
> Is there a function that allows users to read a trajectory file and print
> it in a readable format (like gmxdump) but starting from a user-specified
> frame rather than from 0?
>
> Thanks in advance,
> Silvia Crivelli
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero

2010-12-01 Thread Silvia Crivelli


Hello,

Is there a function that allows users to read a trajectory file and  
print it in a readable format (like gmxdump) but starting from a user- 
specified frame rather than from 0?


Thanks in advance,
Silvia Crivelli
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Cut-offs using CHARMM27 ff

2010-12-01 Thread Hassan Shallal

Dear Gromacs users,
 
I am trying to use CHARMM27 taking the simulation conditions of two recent 
articles as guides in optimizing the simulation parameters. (DOI: 
10.1021/ct900549r and DOI: 10.1021/jp101581h). 
 
-- Both are using PME for electrostatics and I am planning to do that too
-- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force field as 
mentioned)
-- In the second paper, they have explicitly assigned rvdw = 1.2 (this value is 
also optimized for CHARMM27 force field) and they assigned the NS rlist = 1.2 
because as I understand, using PME as a coulombtype requires rcoulomb to be 
equal to rlist. I have no problem following up until now and it seems that 
(rlist = rcoulomb = rvdw = 1.2) presents the best combination of cut-offs for 
using (coulombtype = PME and vdwtype = cut-off) along with CHARMM27
 
-- What I can't get is that in the first paper, they mentioned the following 
"van der Waals interactions were switched off between 1.0 to 1.2 nm"
what does that mean in terms of cut-offs and vdwtype?
Does that mean vdwtype = switch, vdw_switch = 1, rvdw = 1.2 ? and if this is 
what is meant, then rlist has to be 0.1-0.3 larger than rvdw to accomodate for 
the size of the charge groups as mentioned in the manual and accordingly, we 
can't keep rcoulomb = 1.2 because rcoulomb must be equal to rlist to allow 
using PME.
 
I am sure I miss something or I misunderstand the above statement (colored 
red). I would really appreciate any help by explaining the above statement 
(colored red) in the context of using CHARMM27 force field with optimized rvdw 
and rcoulomb both equal to 1.2 nm and using PME for electrostatics.
 
Thanks
Hassan 
 
 
 
 
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] RE:C6 attractive term off OPLSAA

Would I change the sigma to negative in my nb.itp file the way it is  
set or do I need to include a [nonbond_params] section and make sigma  
negative in that specific section? because I realize from the manual  
OPLS-AA uses combination rule 3 but in the manual it shows to combine  
sigma for i and j using rule 2 and rule 1 and 3 correspond to C6 and  
C12 for i and j. Is that correct?


Quoting nishap.pa...@utoronto.ca:


I am going to give that a try. Thanks.


Quoting Berk Hess :



Hi,

Maybe it is not so clear from the topology table in the manual, but  
  when you supply

sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params
section also expects sigma and epsilon.
So it seems you could not set only C6 to zero.
However there is an, undocumented, trick: if you use a negative sigma,
C6 is set to zero.

Berk


Date: Wed, 1 Dec 2010 10:42:11 -0500
From: nishap.pa...@utoronto.ca
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] C6 attractive term off OPLSAA

I see. I actually want to compare my RDFs with C6 term off. Earlier I
tried using force.c code file and turned C6 = 0, but when i compared
my RDFs, it didn't look any different so I am not sure if it even
worked at all or made any difference to the simulation, but again I
was using OPLS-AA and the nb.itp file itself does not indicate value
for C6 or C12.

If there any other way I could achieve this?



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

I ran the simulation using a different force field ffG53a6. I
modified the ffG53a6nb.itp file by changing the term C6 to zero for
 nonbonded parameters, but this time for urea in water. The
simulation ran fine without any warning or exploding. I don't
understand why it would work with one force-field and not with
OPLS-AA.



I don't understand why it worked at all, frankly, but more than likely
you've been lucky enough to make 53a6 work, but OPLS-AA failed.  You're
making significant alterations to the nonbonded interactions of the
system.


Also using mdrun -rerun, I would basically use the nb.itp file with
 nonbonded parameters as mentioned earlier and everything else is
the same i.e. my .mdp parameters and do another run using my
previous trajectory file? I tried to look through some of the posts
 for using -rerun but I don't understand how that would not still
blow up the system. I would like to give it a try for sure but I am
 not quite sure how I would use the command as such.



Using mdrun -rerun recalculates energies from an existing trajectory.
You would generate a trajectory with a normal force field model, then
create a new .tpr file that has your modified potential, such that you
can decompose the energy terms cleverly.  If your goal is to generate
trajectories to study the effects of using a modified potential (i.e.,
C6 = 0), then you can't use -rerun.

-Justin


I really appreciate the help.

Thanks.


Quoting Mark Abraham :


On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:



nishap.pa...@utoronto.ca wrote:

I tried using the nonbonded parameters as defined below in my
ffoplsaanb.itp file for methanol in water and this is the syntax
 I  used:

[nonbond_params]
;ijfuncc6c12
opls_154opls_11110.00E+0002.43E-006
opls_154opls_11210.00E+0000.00E+000
opls_154opls_112  10.00E+0000.00E+000
opls_155opls_111  10.00E+0000.00E+000
opls_155opls_112  10.00E+0000.00E+000
opls_155opls_112  10.00E+0000.00E+000
opls_156opls_111  10.00E+0002.70E-007
opls_156opls_112  10.00E+0000.00E+000
opls_156opls_11210.00E+0000.00E+000
opls_157opls_111  10.00E+0003.01E-006
opls_157opls_112  10.00E+0000.00E+000

When I tried to do mdrun, I got an error saying my system is
exploding. I tried doing the mdrun without nonbonded parameters
 and it runs fine. So I am not sure if I am using the
nonbond_params concept correctly. i.e. I want C6 to be zero
between my solute (methanol) and solvent (water). This is the
error:

Warning: 1-4 interaction between 2 and 6 at distance 3.786 which
  is larger than the 1-4 table size 2.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Suggestions?



Your implementation of your concept is technically correct, but
perhaps physically unreasonable.  You're turning off the
attractive  LJ component and leaving only a repulsive component.
 It sounds  about right that everything is flying apart.


Indeed. The way to do this is with mdrun -rerun on a trajectory
generated with the normal version of the forcefield, as I think I said
in another thread yesterday.

Mark



-Justin


Thanks.

-Nisha P

Quoting nishap.pa...@utoronto.ca:


Okay I am going to give it a try. I just wanted to make sure I was
calculating C6 and C12 correctly as well using sigm

[gmx-users] Re:Re: Re:RE:Re-installation(4.5.3) mdrun crashes? (Justin A. Lemkul)

2010-12-01 Thread lloyd riggs

Dear All,

> If you suspect a faulty installation, then you need to post more
> information, like:
> 
> - compilers used
> - cmake or autoconf?
> - hardware
> - commands used to install
> 
> -Justin
> 
> > Sincerely
> > 
> > Stephan Watkins
> > 


Compilers are all standard gnu compilers

I used autoconf with the commmands:

1) ./config --disable-float --enable-shared --prefix=$HOME --fftw=fftw3

-normal make, make install , then make distclean

2)./config --disable-float --enable-shared --prefix=$HOME --fftw=fftw3 
--enable-mpi

-make mdrun , make install-mdrun

-Hardware, University of Bern Ubelix system, main server is a normal intel i5 
processor I believe, with 4 processors, but not sure, using arch and is 
attached to the main hub of 1200 cpus aranged in 8 cpu nodes (ranging from 8 
AMD 6 core, to 8 older intel chips xeon or other), and secoundary 1200 CPU 
system (nordugrid), which is about the same, but more higher end chips at the 
moment.

-gromacs is installed local, with shared libraries.  All the commands print the 
help menu's

-as mentioned to the University cluster folks, I am not sure if it is the 
gromacs libraries, or the main shared libraries mentioned in the error, or 
something else.  I mean it looks like memory addresses read-write error's to 
me, but I ain't much of a system maintainer so don't know if it is a 
compilation error, something buggy on this system with the new gromacs, or if 
something changed in the libraries on the local machine.

Sincerely,

Stephan Watkins
-- 
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!  
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

RE: [gmx-users] C6 attractive term off OPLSAA


I am going to give that a try. Thanks.


Quoting Berk Hess :



Hi,

Maybe it is not so clear from the topology table in the manual, but   
when you supply

sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params
section also expects sigma and epsilon.
So it seems you could not set only C6 to zero.
However there is an, undocumented, trick: if you use a negative sigma,
C6 is set to zero.

Berk


Date: Wed, 1 Dec 2010 10:42:11 -0500
From: nishap.pa...@utoronto.ca
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] C6 attractive term off OPLSAA

I see. I actually want to compare my RDFs with C6 term off. Earlier I
tried using force.c code file and turned C6 = 0, but when i compared
my RDFs, it didn't look any different so I am not sure if it even
worked at all or made any difference to the simulation, but again I
was using OPLS-AA and the nb.itp file itself does not indicate value
for C6 or C12.

If there any other way I could achieve this?



Quoting "Justin A. Lemkul" :

>
>
> nishap.pa...@utoronto.ca wrote:
>> I ran the simulation using a different force field ffG53a6. I
>> modified the ffG53a6nb.itp file by changing the term C6 to zero for
>>  nonbonded parameters, but this time for urea in water. The
>> simulation ran fine without any warning or exploding. I don't
>> understand why it would work with one force-field and not with
>> OPLS-AA.
>>
>
> I don't understand why it worked at all, frankly, but more than likely
> you've been lucky enough to make 53a6 work, but OPLS-AA failed.  You're
> making significant alterations to the nonbonded interactions of the
> system.
>
>> Also using mdrun -rerun, I would basically use the nb.itp file with
>>  nonbonded parameters as mentioned earlier and everything else is
>> the same i.e. my .mdp parameters and do another run using my
>> previous trajectory file? I tried to look through some of the posts
>>  for using -rerun but I don't understand how that would not still
>> blow up the system. I would like to give it a try for sure but I am
>>  not quite sure how I would use the command as such.
>>
>
> Using mdrun -rerun recalculates energies from an existing trajectory.
> You would generate a trajectory with a normal force field model, then
> create a new .tpr file that has your modified potential, such that you
> can decompose the energy terms cleverly.  If your goal is to generate
> trajectories to study the effects of using a modified potential (i.e.,
> C6 = 0), then you can't use -rerun.
>
> -Justin
>
>> I really appreciate the help.
>>
>> Thanks.
>>
>>
>> Quoting Mark Abraham :
>>
>>> On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:


 nishap.pa...@utoronto.ca wrote:
> I tried using the nonbonded parameters as defined below in my
> ffoplsaanb.itp file for methanol in water and this is the syntax
>  I  used:
>
> [nonbond_params]
> ;ijfuncc6c12
> opls_154opls_11110.00E+0002.43E-006
> opls_154opls_11210.00E+0000.00E+000
> opls_154opls_112  10.00E+0000.00E+000
> opls_155opls_111  10.00E+0000.00E+000
> opls_155opls_112  10.00E+0000.00E+000
> opls_155opls_112  10.00E+0000.00E+000
> opls_156opls_111  10.00E+0002.70E-007
> opls_156opls_112  10.00E+0000.00E+000
> opls_156opls_11210.00E+0000.00E+000
> opls_157opls_111  10.00E+0003.01E-006
> opls_157opls_112  10.00E+0000.00E+000
>
> When I tried to do mdrun, I got an error saying my system is
> exploding. I tried doing the mdrun without nonbonded parameters
>  and it runs fine. So I am not sure if I am using the
> nonbond_params concept correctly. i.e. I want C6 to be zero
> between my solute (methanol) and solvent (water). This is the
> error:
>
> Warning: 1-4 interaction between 2 and 6 at distance 3.786 which
>   is larger than the 1-4 table size 2.500 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> Suggestions?
>

 Your implementation of your concept is technically correct, but
 perhaps physically unreasonable.  You're turning off the
 attractive  LJ component and leaving only a repulsive component.
  It sounds  about right that everything is flying apart.
>>>
>>> Indeed. The way to do this is with mdrun -rerun on a trajectory
>>> generated with the normal version of the forcefield, as I think I said
>>> in another thread yesterday.
>>>
>>> Mark
>>>

 -Justin

> Thanks.
>
> -Nisha P
>
> Quoting nishap.pa...@utoronto.ca:
>
>> Okay I am going to give it a try. I just wanted to make sure I was
>> calculating C6 and C12 correctly as well using sigma and epsilon
>> accord

RE: [gmx-users] C6 attractive term off OPLSAA

2010-12-01 Thread Berk Hess


Hi,

Maybe it is not so clear from the topology table in the manual, but when you 
supply
sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params
section also expects sigma and epsilon.
So it seems you could not set only C6 to zero.
However there is an, undocumented, trick: if you use a negative sigma,
C6 is set to zero.

Berk

> Date: Wed, 1 Dec 2010 10:42:11 -0500
> From: nishap.pa...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] C6 attractive term off OPLSAA
> 
> I see. I actually want to compare my RDFs with C6 term off. Earlier I  
> tried using force.c code file and turned C6 = 0, but when i compared  
> my RDFs, it didn't look any different so I am not sure if it even  
> worked at all or made any difference to the simulation, but again I  
> was using OPLS-AA and the nb.itp file itself does not indicate value  
> for C6 or C12.
> 
> If there any other way I could achieve this?
> 
> 
> 
> Quoting "Justin A. Lemkul" :
> 
> >
> >
> > nishap.pa...@utoronto.ca wrote:
> >> I ran the simulation using a different force field ffG53a6. I   
> >> modified the ffG53a6nb.itp file by changing the term C6 to zero for  
> >>  nonbonded parameters, but this time for urea in water. The   
> >> simulation ran fine without any warning or exploding. I don't   
> >> understand why it would work with one force-field and not with   
> >> OPLS-AA.
> >>
> >
> > I don't understand why it worked at all, frankly, but more than likely
> > you've been lucky enough to make 53a6 work, but OPLS-AA failed.  You're
> > making significant alterations to the nonbonded interactions of the
> > system.
> >
> >> Also using mdrun -rerun, I would basically use the nb.itp file with  
> >>  nonbonded parameters as mentioned earlier and everything else is   
> >> the same i.e. my .mdp parameters and do another run using my   
> >> previous trajectory file? I tried to look through some of the posts  
> >>  for using -rerun but I don't understand how that would not still   
> >> blow up the system. I would like to give it a try for sure but I am  
> >>  not quite sure how I would use the command as such.
> >>
> >
> > Using mdrun -rerun recalculates energies from an existing trajectory.
> > You would generate a trajectory with a normal force field model, then
> > create a new .tpr file that has your modified potential, such that you
> > can decompose the energy terms cleverly.  If your goal is to generate
> > trajectories to study the effects of using a modified potential (i.e.,
> > C6 = 0), then you can't use -rerun.
> >
> > -Justin
> >
> >> I really appreciate the help.
> >>
> >> Thanks.
> >>
> >>
> >> Quoting Mark Abraham :
> >>
> >>> On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:
> 
> 
>  nishap.pa...@utoronto.ca wrote:
> > I tried using the nonbonded parameters as defined below in my
> > ffoplsaanb.itp file for methanol in water and this is the syntax  
> >  I  used:
> >
> > [nonbond_params]
> > ;ijfuncc6c12
> > opls_154opls_11110.00E+0002.43E-006
> > opls_154opls_11210.00E+0000.00E+000
> > opls_154opls_112  10.00E+0000.00E+000
> > opls_155opls_111  10.00E+0000.00E+000
> > opls_155opls_112  10.00E+0000.00E+000
> > opls_155opls_112  10.00E+0000.00E+000
> > opls_156opls_111  10.00E+0002.70E-007
> > opls_156opls_112  10.00E+0000.00E+000
> > opls_156opls_11210.00E+0000.00E+000
> > opls_157opls_111  10.00E+0003.01E-006
> > opls_157opls_112  10.00E+0000.00E+000
> >
> > When I tried to do mdrun, I got an error saying my system is
> > exploding. I tried doing the mdrun without nonbonded parameters   
> >  and it runs fine. So I am not sure if I am using the
> > nonbond_params concept correctly. i.e. I want C6 to be zero
> > between my solute (methanol) and solvent (water). This is the   
> > error:
> >
> > Warning: 1-4 interaction between 2 and 6 at distance 3.786 which  
> >   is larger than the 1-4 table size 2.500 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding,
> > if not, you should increase table-extension in your mdp file
> > or with user tables increase the table size
> >
> > Suggestions?
> >
> 
>  Your implementation of your concept is technically correct, but
>  perhaps physically unreasonable.  You're turning off the   
>  attractive  LJ component and leaving only a repulsive component.   
>   It sounds  about right that everything is flying apart.
> >>>
> >>> Indeed. The way to do this is with mdrun -rerun on a trajectory
> >>> generated with the normal version of the forcefield, as I think I said
> >>> in another thread yesterday.
> >>>
> >>> Mark
> >>>
> 
>  -Justin
> 
> > Thanks.

Re: [gmx-users] air-water interface


On 2/12/2010 12:30 AM, 铁锋 彭 wrote:

Hi, everyone
I find that i used T and P coupling in water-air interface, that is 
the reason my system imploded.

So i changed to NVT. But there are still fatal errors.
I have some questions concerning  .gro file.
for example in spc216.gro, there are both + and - psotions. But in 
other .gro file, all is + postion.

What is the difference between .gro ?



If the system is periodic, what does the sign matter?

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/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] Reg: Standard error


On 1/12/2010 8:25 PM, vinothkumar mohanakrishnan wrote:

Dear Mark

Thank you for your explaination but Its not clear to me what you are 
trying to say. can you explain it bit more clearly. what should i need 
to do to get the standard error? any help is highly appreciated.


Like I said, you need to make independent measurements of a quantity to 
form an estimate of the mean, and thus an estimate of the standard 
deviation among such estimates (i.e. standard error of the mean). This 
is pretty basic scientific statistics. Your MD steps are all correlated 
because of how they were generated, so you need to look at the 
autocorrelation time (Google!) of your observable to get a starting idea 
of how many actual independent measurements your data represents.


Mark



Regards
Vinoth

On Wed, Dec 1, 2010 at 2:39 PM, Mark Abraham > wrote:


On 1/12/2010 7:59 PM, vinothkumar mohanakrishnan wrote:

Hi Gromacians

I am planning to compute the standard error for the
interfacial surface tension of water-dichloro ethane. i just
want to know is my procedure right. below is the result what i
get from my g_energy command.

Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1
data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.
 Drift  Tot-Drift


---
#Surf*SurfTen   692.9044579.464579.16
 -0.181601   -181.602

my question is to calculate the standard error should i need
to divide the RMSD(4579.46) by the squareroot of 51 steps?
any help is highly appreciated.


Calculating the standard error of the mean in this way requires
that the observations are independent
(http://en.wikipedia.org/wiki/Standard_error_%28statistics%29).
Adjacent MD frames are not. You would need to know something about
your correlation times to know how long you have to wait before
effective independence.

Mark
-- 
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/Support/Mailing_Lists/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/Support/Mailing_Lists




-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] C6 attractive term off OPLSAA

I see. I actually want to compare my RDFs with C6 term off. Earlier I  
tried using force.c code file and turned C6 = 0, but when i compared  
my RDFs, it didn't look any different so I am not sure if it even  
worked at all or made any difference to the simulation, but again I  
was using OPLS-AA and the nb.itp file itself does not indicate value  
for C6 or C12.


If there any other way I could achieve this?



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:
I ran the simulation using a different force field ffG53a6. I   
modified the ffG53a6nb.itp file by changing the term C6 to zero for  
 nonbonded parameters, but this time for urea in water. The   
simulation ran fine without any warning or exploding. I don't   
understand why it would work with one force-field and not with   
OPLS-AA.




I don't understand why it worked at all, frankly, but more than likely
you've been lucky enough to make 53a6 work, but OPLS-AA failed.  You're
making significant alterations to the nonbonded interactions of the
system.

Also using mdrun -rerun, I would basically use the nb.itp file with  
 nonbonded parameters as mentioned earlier and everything else is   
the same i.e. my .mdp parameters and do another run using my   
previous trajectory file? I tried to look through some of the posts  
 for using -rerun but I don't understand how that would not still   
blow up the system. I would like to give it a try for sure but I am  
 not quite sure how I would use the command as such.




Using mdrun -rerun recalculates energies from an existing trajectory.
You would generate a trajectory with a normal force field model, then
create a new .tpr file that has your modified potential, such that you
can decompose the energy terms cleverly.  If your goal is to generate
trajectories to study the effects of using a modified potential (i.e.,
C6 = 0), then you can't use -rerun.

-Justin


I really appreciate the help.

Thanks.


Quoting Mark Abraham :


On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:



nishap.pa...@utoronto.ca wrote:
I tried using the nonbonded parameters as defined below in my
ffoplsaanb.itp file for methanol in water and this is the syntax  
 I  used:


[nonbond_params]
;ijfuncc6c12
opls_154opls_11110.00E+0002.43E-006
opls_154opls_11210.00E+0000.00E+000
opls_154opls_112  10.00E+0000.00E+000
opls_155opls_111  10.00E+0000.00E+000
opls_155opls_112  10.00E+0000.00E+000
opls_155opls_112  10.00E+0000.00E+000
opls_156opls_111  10.00E+0002.70E-007
opls_156opls_112  10.00E+0000.00E+000
opls_156opls_11210.00E+0000.00E+000
opls_157opls_111  10.00E+0003.01E-006
opls_157opls_112  10.00E+0000.00E+000

When I tried to do mdrun, I got an error saying my system is
exploding. I tried doing the mdrun without nonbonded parameters   
 and it runs fine. So I am not sure if I am using the
nonbond_params concept correctly. i.e. I want C6 to be zero
between my solute (methanol) and solvent (water). This is the   
error:


Warning: 1-4 interaction between 2 and 6 at distance 3.786 which  
  is larger than the 1-4 table size 2.500 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Suggestions?



Your implementation of your concept is technically correct, but
perhaps physically unreasonable.  You're turning off the   
attractive  LJ component and leaving only a repulsive component.   
 It sounds  about right that everything is flying apart.


Indeed. The way to do this is with mdrun -rerun on a trajectory
generated with the normal version of the forcefield, as I think I said
in another thread yesterday.

Mark



-Justin


Thanks.

-Nisha P

Quoting nishap.pa...@utoronto.ca:


Okay I am going to give it a try. I just wanted to make sure I was
calculating C6 and C12 correctly as well using sigma and epsilon
according to rule 3

C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon

Thanks


Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

I have a concern regarding C6 attractive term in LJ   
potential.  I  am using OPLS-AA force field, and I wish to   
turn off  attractive   term C6 by setting the parameters to   
zero. One of  the suggestion   was to add a [nonbond_params]   
in my  ffoplsaanb.itp file and set  the  C6 to zero between   
the  non-bonded pair. In my system for  example,  which   
consists of  one methanol in water, I wish to set  C6 term to  
  zero between  my solute and solvent. Since OPLSAA is  all   
atom force  field  it treats each atom individually and has
sigma and epsilon   for each atom, so I am not sure how I   
would  actually set my   nonbond_params in my nb.itp file. I   
realize I  need to convert  each  sigma and epsilon to C6 and  
 C12, so sa

Re: [gmx-users] C6 attractive term off OPLSAA




nishap.pa...@utoronto.ca wrote:
I ran the simulation using a different force field ffG53a6. I modified 
the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded 
parameters, but this time for urea in water. The simulation ran fine 
without any warning or exploding. I don't understand why it would work 
with one force-field and not with OPLS-AA.




I don't understand why it worked at all, frankly, but more than likely you've 
been lucky enough to make 53a6 work, but OPLS-AA failed.  You're making 
significant alterations to the nonbonded interactions of the system.


Also using mdrun -rerun, I would basically use the nb.itp file with 
nonbonded parameters as mentioned earlier and everything else is the 
same i.e. my .mdp parameters and do another run using my previous 
trajectory file? I tried to look through some of the posts for using 
-rerun but I don't understand how that would not still blow up the 
system. I would like to give it a try for sure but I am not quite sure 
how I would use the command as such.




Using mdrun -rerun recalculates energies from an existing trajectory.  You would 
generate a trajectory with a normal force field model, then create a new .tpr 
file that has your modified potential, such that you can decompose the energy 
terms cleverly.  If your goal is to generate trajectories to study the effects 
of using a modified potential (i.e., C6 = 0), then you can't use -rerun.


-Justin


I really appreciate the help.

Thanks.


Quoting Mark Abraham :


On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:



nishap.pa...@utoronto.ca wrote:
I tried using the nonbonded parameters as defined below in my  
ffoplsaanb.itp file for methanol in water and this is the syntax I 
 used:


[nonbond_params]
;ijfuncc6c12
 opls_154opls_11110.00E+0002.43E-006
 opls_154opls_11210.00E+0000.00E+000
 opls_154opls_112  10.00E+0000.00E+000
 opls_155opls_111  10.00E+0000.00E+000
 opls_155opls_112  10.00E+0000.00E+000
 opls_155opls_112  10.00E+0000.00E+000
 opls_156opls_111  10.00E+0002.70E-007
 opls_156opls_112  10.00E+0000.00E+000
 opls_156opls_11210.00E+0000.00E+000
 opls_157opls_111  10.00E+0003.01E-006
 opls_157opls_112  10.00E+0000.00E+000

When I tried to do mdrun, I got an error saying my system is  
exploding. I tried doing the mdrun without nonbonded parameters  and 
it runs fine. So I am not sure if I am using the  nonbond_params 
concept correctly. i.e. I want C6 to be zero  between my solute 
(methanol) and solvent (water). This is the error:


Warning: 1-4 interaction between 2 and 6 at distance 3.786 which  is 
larger than the 1-4 table size 2.500 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Suggestions?



Your implementation of your concept is technically correct, but  
perhaps physically unreasonable.  You're turning off the attractive 
 LJ component and leaving only a repulsive component.  It sounds  
about right that everything is flying apart.


Indeed. The way to do this is with mdrun -rerun on a trajectory
generated with the normal version of the forcefield, as I think I said
in another thread yesterday.

Mark



-Justin


Thanks.

-Nisha P

Quoting nishap.pa...@utoronto.ca:


Okay I am going to give it a try. I just wanted to make sure I was
calculating C6 and C12 correctly as well using sigma and epsilon
according to rule 3

C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon

Thanks


Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

I have a concern regarding C6 attractive term in LJ potential.  
I  am using OPLS-AA force field, and I wish to turn off  
attractive   term C6 by setting the parameters to zero. One of  
the suggestion   was to add a [nonbond_params] in my  
ffoplsaanb.itp file and set  the  C6 to zero between the  
non-bonded pair. In my system for  example,  which consists of  
one methanol in water, I wish to set  C6 term to  zero between  
my solute and solvent. Since OPLSAA is  all atom force  field  it 
treats each atom individually and has  sigma and epsilon   for 
each atom, so I am not sure how I would  actually set my   
nonbond_params in my nb.itp file. I realize I  need to convert  
each  sigma and epsilon to C6 and C12, so say for  example for  
methanol in  water my [nonbond_params] would look  something  
like this?


[ nonbond_params ]
; ij func  c6   c12
   CTOW  1   0.00  calculated value for C12 here?
   CTHW1  1  0.00
   CTHW2  1  0.00

CT is the carbon in Methanol. OW, HW1 an HW2 correspond to  
atoms  in  TIP3P water model


Is that correct? Would I have to do that for each atom in methanol?



Sounds about right to me.

-Justin


Any suggestions would be ap

Re: [gmx-users] C6 attractive term off OPLSAA

I ran the simulation using a different force field ffG53a6. I modified  
the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded  
parameters, but this time for urea in water. The simulation ran fine  
without any warning or exploding. I don't understand why it would work  
with one force-field and not with OPLS-AA.


Also using mdrun -rerun, I would basically use the nb.itp file with  
nonbonded parameters as mentioned earlier and everything else is the  
same i.e. my .mdp parameters and do another run using my previous  
trajectory file? I tried to look through some of the posts for using  
-rerun but I don't understand how that would not still blow up the  
system. I would like to give it a try for sure but I am not quite sure  
how I would use the command as such.


I really appreciate the help.

Thanks.


Quoting Mark Abraham :


On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:



nishap.pa...@utoronto.ca wrote:
I tried using the nonbonded parameters as defined below in my   
ffoplsaanb.itp file for methanol in water and this is the syntax I  
 used:


[nonbond_params]
;ijfuncc6c12
 opls_154opls_11110.00E+0002.43E-006
 opls_154opls_11210.00E+0000.00E+000
 opls_154opls_112  10.00E+0000.00E+000
 opls_155opls_111  10.00E+0000.00E+000
 opls_155opls_112  10.00E+0000.00E+000
 opls_155opls_112  10.00E+0000.00E+000
 opls_156opls_111  10.00E+0002.70E-007
 opls_156opls_112  10.00E+0000.00E+000
 opls_156opls_11210.00E+0000.00E+000
 opls_157opls_111  10.00E+0003.01E-006
 opls_157opls_112  10.00E+0000.00E+000

When I tried to do mdrun, I got an error saying my system is   
exploding. I tried doing the mdrun without nonbonded parameters   
and it runs fine. So I am not sure if I am using the   
nonbond_params concept correctly. i.e. I want C6 to be zero   
between my solute (methanol) and solvent (water). This is the error:


Warning: 1-4 interaction between 2 and 6 at distance 3.786 which   
is larger than the 1-4 table size 2.500 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Suggestions?



Your implementation of your concept is technically correct, but   
perhaps physically unreasonable.  You're turning off the attractive  
 LJ component and leaving only a repulsive component.  It sounds   
about right that everything is flying apart.


Indeed. The way to do this is with mdrun -rerun on a trajectory
generated with the normal version of the forcefield, as I think I said
in another thread yesterday.

Mark



-Justin


Thanks.

-Nisha P

Quoting nishap.pa...@utoronto.ca:


Okay I am going to give it a try. I just wanted to make sure I was
calculating C6 and C12 correctly as well using sigma and epsilon
according to rule 3

C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon

Thanks


Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

I have a concern regarding C6 attractive term in LJ potential.   
I  am using OPLS-AA force field, and I wish to turn off   
attractive   term C6 by setting the parameters to zero. One of   
the suggestion   was to add a [nonbond_params] in my   
ffoplsaanb.itp file and set  the  C6 to zero between the   
non-bonded pair. In my system for  example,  which consists of   
one methanol in water, I wish to set  C6 term to  zero between   
my solute and solvent. Since OPLSAA is  all atom force  field   
it treats each atom individually and has  sigma and epsilon
for each atom, so I am not sure how I would  actually set my
nonbond_params in my nb.itp file. I realize I  need to convert   
each  sigma and epsilon to C6 and C12, so say for  example for   
methanol in  water my [nonbond_params] would look  something   
like this?


[ nonbond_params ]
; ij func  c6   c12
   CTOW  1   0.00  calculated value for C12 here?
   CTHW1  1  0.00
   CTHW2  1  0.00

CT is the carbon in Methanol. OW, HW1 an HW2 correspond to   
atoms  in  TIP3P water model


Is that correct? Would I have to do that for each atom in methanol?



Sounds about right to me.

-Justin


Any suggestions would be appreciated.

Thanks.

Nisha P



--


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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to

Re: [gmx-users] Re:Re-installation(4.5.3) mdrun crashes?




lloyd riggs wrote:

Dear All, (this is a repost as I included no subjectline)

I have the following error, for both mpi and normal mdrun modes.  I tried both 
using a pull group for the first time, but when the error persisted, went back 
and used data/md.mdp files which I know work as a test and get the same errors.


[anode27:16555] *** Process received signal ***
[anode27:16555] Signal: Segmentation fault (11)
[anode27:16555] Signal code: Address not mapped (1)
[anode27:16555] Failing at address: 0x2b56a416a530
[anode27:16555] [ 0] /lib/libpthread.so.0(+0xf010) [0x2b5687981010]
[anode27:16555] [ 1]

/home/ubelix/l_insel_ria/l_watkins/lib/libgmx_mpi_d.so.6(+0x20303c) 
[0x2b56867d603c]

[anode27:16555] *** End of error message ***


and then a complete core dump.

If I run an em , it runs, but does not do anything (start=finish).

I had installed the newest version 4.5.3 a few weeks back, and just realized 
something has gone wrong, as I used em's to test quickly, but only looked to 
see if it gave the output files (I mean they were the correct sizes as it runs 
50-100 iterations with nothing in any field, such as pressure, energy, 
etc...and then says converged).

Does anyone know how to fix this?



If you suspect a faulty installation, then you need to post more information, 
like:

- compilers used
- cmake or autoconf?
- hardware
- commands used to install

-Justin


Sincerely

Stephan Watkins



--


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/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Re:Re-installation(4.5.3) mdrun crashes?

2010-12-01 Thread lloyd riggs

Dear All, (this is a repost as I included no subjectline)

I have the following error, for both mpi and normal mdrun modes.  I tried both 
using a pull group for the first time, but when the error persisted, went back 
and used data/md.mdp files which I know work as a test and get the same errors.

> >
> > [anode27:16555] *** Process received signal ***
> > [anode27:16555] Signal: Segmentation fault (11)
> > [anode27:16555] Signal code: Address not mapped (1)
> > [anode27:16555] Failing at address: 0x2b56a416a530
> > [anode27:16555] [ 0] /lib/libpthread.so.0(+0xf010) [0x2b5687981010]
> > [anode27:16555] [ 1]
> /home/ubelix/l_insel_ria/l_watkins/lib/libgmx_mpi_d.so.6(+0x20303c) 
> [0x2b56867d603c]
> > [anode27:16555] *** End of error message ***

and then a complete core dump.

If I run an em , it runs, but does not do anything (start=finish).

I had installed the newest version 4.5.3 a few weeks back, and just realized 
something has gone wrong, as I used em's to test quickly, but only looked to 
see if it gave the output files (I mean they were the correct sizes as it runs 
50-100 iterations with nothing in any field, such as pressure, energy, 
etc...and then says converged).

Does anyone know how to fix this?

Sincerely

Stephan Watkins

-- 
GMX DSL Doppel-Flat ab 19,99 €/mtl.! Jetzt auch mit 
gratis Notebook-Flat! http://portal.gmx.net/de/go/dsl
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

RE: [gmx-users] v-rescale and conserved energy

2010-12-01 Thread Berk Hess


Hi,

The integrator is not the issue. The cut-off setup is. 
You should use interactions that go smoothly to zero with a buffer region in 
the neighborlist.
Use for instance shift for LJ interactions. PME could be switched, but that is 
a much smaller
contribution. Use rlist about 0.3 nm larger than rvdw (and rcoulomb if you 
switch PME).
Note that your current cut-off's are overly long.

All this probably doesn't matter much for the surface tension.

PS spatially isotropic dispersion correction does not work for the surface 
tension,
you need to determine the dispersion correction to the surface tension 
analytically.

Berk

From: mstu...@slb.com
To: gmx-users@gromacs.org
Date: Wed, 1 Dec 2010 12:10:23 +
Subject: [gmx-users] v-rescale and conserved energy



Dear gromacs users, I am running NVT simulations for polarizable (shell 
particle) water model  (GROMACS version 4.5.1 and 4.5.3 (issue is same in 
both)) using v-rescale thermostat. While temperature, potential, kinetic and 
total energies behave quite well I am failing to obtain constant values for 
Conserved-Energy. It drifts quite significantly: 1000 kJ/mol/ns with average 
value 32500 kJ/mol.I have  noticed that this issue has been already addressed: 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html So I tried 
to switch from  md (leap-frog)  to md-vv integrator, but then temperature went 
up enormously  According to 
http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.htmlthis issue seems 
also be know , but I have not found if it  was fixed in 4.5.x version? Am I 
doing something obviously wrong? And should Conserved-Energy drift be a real 
problem if the purpose of the simulation is calculation of the surface tension? 
 My .mdp file is shown below. Thank you very much in advance.Mikhail 
===integrator  =  md or md-vvdt 
 =  0.001; time stepnsteps  =  2000 
; number of stepscomm_mode   =  Linear;Angular   ; Remove 
center of mass translation and rotationnstcomm =  1003  
   ; reset c.o.m. motionnstxout =  1; write 
coordsnstvout =  1  ; write velocitiesnstxtcout 
  =  1000  ; write coords to xtc-trajectory filenstlog  
=  1000 ; print to logfilenstlist = 
 20   ; update pairlistns_type =  grid ;simple  
   ; pairlist method;== Polarizable model parameters 
===emtol   =  0.001  ;the 
convergency criterion for maximum forceniter   =  50
;maximum number of iterations for the shell particle 
optimization;=  SHAKE/SETTLE Specification  
===shake_tol= 0.1;= 
 Cutt off specification =pbc = xyz  
 ; periodic boundary conditionsoptimize_fft=  yes   
   ; perform FFT optimization at startcoulombtype =  
PMEewald_geometry  =  3dcrcoulomb=  1.5 ;1.5 ; 
cut-off for coulombrlist   =  1.5 ;1.5 ; cut-off 
for nsvdw-type=  cut-offrvdw=  1.5 ;1.5 
; cut-off for vdwdispcorr=  
EnerPres;===Tcoupl
  =  v-rescale ;; temperature couplingtc-grps = 
 Systemref_t   =  298.15tau_t   =  0.1Pcoupl
  =  
no;===gen_vel
 =  no   ; generate initial velocitiesgen_temp  
  =  300  ; initial temperaturegen_seed
=  -1   ; random seed 
===   
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists   
  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 6

2010-12-01 Thread lloyd riggs

Dear All,

I have the following error, for both mpi and normal mdrun modes.  I tried both 
using a pull group for the first time, but when the error persisted, went back 
and used data/md.mdp files which I know work as a test and get the same errors.

> >
> > [anode27:16555] *** Process received signal ***
> > [anode27:16555] Signal: Segmentation fault (11)
> > [anode27:16555] Signal code: Address not mapped (1)
> > [anode27:16555] Failing at address: 0x2b56a416a530
> > [anode27:16555] [ 0] /lib/libpthread.so.0(+0xf010) [0x2b5687981010]
> > [anode27:16555] [ 1]
> /home/ubelix/l_insel_ria/l_watkins/lib/libgmx_mpi_d.so.6(+0x20303c) 
> [0x2b56867d603c]
> > [anode27:16555] *** End of error message ***

and then a complete core dump.

If I run an em , it runs, but does not do anything (start=finish).

I had installed the newest version 4.5.3 a few weeks back, and just realized 
something has gone wrong, as I used em's to test quickly, but only looked to 
see if it gave the output files (I mean they were the correct sizes).

Does anyone know how to fix this?

Sincerely

Stephan Watkins


-- 
GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern
E-Mail & mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] air-water interface

2010-12-01 Thread 铁锋彭

Hi, everyone
 
I find that i used T and P coupling in water-air interface, that is the reason 
my system imploded. 
 
So i changed to NVT. But there are still fatal errors.
 
I have some questions concerning  .gro file.
 
for example in spc216.gro, there are both + and - psotions. But in other .gro 
file, all is + postion.
 
What is the difference between .gro ?
 
Thanks


  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] v-rescale and conserved energy

2010-12-01 Thread Mikhail Stukan

Dear gromacs users,

I am running NVT simulations for polarizable (shell particle) water model  
(GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale 
thermostat.
While temperature, potential, kinetic and total energies behave quite well I am 
failing to obtain constant values for Conserved-Energy. It drifts quite 
significantly: 1000 kJ/mol/ns with average value 32500 kJ/mol.
I have  noticed that this issue has been already addressed:

http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041836.html

So I tried to switch from  md (leap-frog)  to md-vv integrator, but then 
temperature went up enormously

According to
http://www.mail-archive.com/gmx-users@gromacs.org/msg32395.html
this issue seems also be know , but I have not found if it  was fixed in 4.5.x 
version?

Am I doing something obviously wrong? And should Conserved-Energy drift be a 
real problem if the purpose of the simulation is calculation of the surface 
tension?

My .mdp file is shown below.

Thank you very much in advance.
Mikhail

===
integrator  =  md or md-vv
dt  =  0.001; time step
nsteps  =  2000 ; number of steps
comm_mode   =  Linear;Angular   ; Remove center of mass 
translation and rotation
nstcomm =  1003 ; reset c.o.m. motion
nstxout =  1; write coords
nstvout =  1  ; write velocities
nstxtcout   =  1000  ; write coords to xtc-trajectory 
file
nstlog  =  1000 ; print to logfile
nstlist =  20   ; update pairlist
ns_type =  grid ;simple ; pairlist method
;== Polarizable model parameters ===
emtol   =  0.001  ;the convergency criterion for 
maximum force
niter   =  50;maximum number of iterations for the 
shell particle optimization
;=  SHAKE/SETTLE Specification  ===
shake_tol= 0.1
;=  Cutt off specification =
pbc = xyz   ; periodic boundary conditions
optimize_fft=  yes  ; perform FFT optimization at 
start
coulombtype =  PME
ewald_geometry  =  3dc
rcoulomb=  1.5 ;1.5 ; cut-off for coulomb
rlist   =  1.5 ;1.5 ; cut-off for ns
vdw-type=  cut-off
rvdw=  1.5 ;1.5 ; cut-off for vdw
dispcorr=  EnerPres
;===
Tcoupl  =  v-rescale ;; temperature coupling
tc-grps =  System
ref_t   =  298.15
tau_t   =  0.1
Pcoupl  =  no
;===
gen_vel =  no   ; generate initial velocities
gen_temp=  300  ; initial temperature
gen_seed=  -1   ; random seed

===



-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] how to specify a location of a molecule in the system




Adva Suez wrote:

Hello all!
I would like to insert a molecule to a membrane system and would like to 
start from a specific position of the molecule (hydrocarbon or lipid 
headgroups). I tried doing that in Pymol after converting the merged gro 
into pdb (using editconf) but when I saved the file in Pymol the order 
of the lipids atoms got mixed up and it does not match the dppc.itp 
anymore. Then it caused problems in grompp.
Do you have another way to set the position of the molecule in the 
system? maybe without converting to PDB...??




You can use editconf -translate/-rotate/-center to manipulate the position of 
the molecule.


-Justin



Thanks,
Adva.

--
Adva Yeheskel
Bioinformatics Unit
Rm 001, Sherman bldg.,
 G.S.W. Faculty of Life Sciences
 Tel-Aviv University, ISRAEL 69978
 
 Tel: 972-3-6406840; Fax: 972-3-6405098

 E-mail: sueza...@tauex.tau.ac.il 
 Web-site: 
http://www.tau.ac.il/lifesci/bioinformatics.html 





--


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/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] Some tools not described any more in online manual




Emanuel Peter wrote:

Dear Gromacs-users,

Could anyone tell me why some analysis-tools as for example anadock, 
g_clustsize and others are not described any more
in the online-manual? Could that mean that these tools are not supported 
any more by the Gromacs community or one should not use them because of 
possible bugs ?




The online manual is very outdated.  I filed a bugzilla noting this fact some 
time ago, but it has not been resolved.


-Justin


Thanks for any suggestions.

Best regards,

Emanuel Peter



--


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/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] Reg: Standard error

2010-12-01 Thread vinothkumar mohanakrishnan

Dear Mark

Thank you for your explaination but Its not clear to me what you are trying
to say. can you explain it bit more clearly. what should i need to do to get
the standard error? any help is highly appreciated.

Regards
Vinoth

On Wed, Dec 1, 2010 at 2:39 PM, Mark Abraham wrote:

> On 1/12/2010 7:59 PM, vinothkumar mohanakrishnan wrote:
>
>> Hi Gromacians
>>
>> I am planning to compute the standard error for the interfacial surface
>> tension of water-dichloro ethane. i just want to know is my procedure right.
>> below is the result what i get from my g_energy command.
>>
>> Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets
>> All averages are exact over 51 steps
>>
>> Energy  Average   RMSD Fluct.  Drift
>>  Tot-Drift
>>
>> ---
>> #Surf*SurfTen   692.9044579.464579.16  -0.181601
>> -181.602
>>
>> my question is to calculate the standard error should i need to divide the
>> RMSD(4579.46) by the squareroot of 51 steps? any help is highly
>> appreciated.
>>
>
> Calculating the standard error of the mean in this way requires that the
> observations are independent (
> http://en.wikipedia.org/wiki/Standard_error_%28statistics%29). Adjacent MD
> frames are not. You would need to know something about your correlation
> times to know how long you have to wait before effective independence.
>
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] Some tools not described any more in online manual

2010-12-01 Thread Emanuel Peter

Dear Gromacs-users,

Could anyone tell me why some analysis-tools as for example anadock, 
g_clustsize and others are not described any more 
in the online-manual? Could that mean that these tools are not supported any 
more by the Gromacs community or one should not use them because of possible 
bugs ? 

Thanks for any suggestions.

Best regards,

Emanuel Peter

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

Re: [gmx-users] Reg: Standard error