date:20120613

I am not going to compare this with anything , I have to look for sequences
and their corresponding energies and select the lowest scoring ones. I
request you to kindly elaborate on freezing some portion of the protein. (
I am bit confused as in my case I am fixing the dihedral of turn residues
which means constraining them simultaneously I want to freeze the other
region of the protein. )


On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham wrote:

>  On 14/06/2012 4:38 PM, bharat gupta wrote:
>
> Thanks Sir for the reply... This question is related to my first query
> that if we constraint the dihedral of the turn residue how can we
> fix/freeze the movement of other residues.
>
>
> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
>
>
>  As I am interested in only getting the energy of the hairpin when the
> turn residues are constrained within a particular phi psi angle range
>
>
> .. and with what are you going to compare those energies? And what will
> that comparison mean?
>
> Mark
>
>
>
>
> On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham wrote:
>
>> On 14/06/2012 12:04 PM, bharat gupta wrote:
>>
>>> Thanks for the reply . Is it possible to calculate the dihedral energy
>>> of certain residues, like in my case for turn residues ??.. How can that be
>>> done
>>>
>>
>>  First, seek to define "dihedral energy"... Force fields are not
>> parametrized such that parts of them are expected to correlate with
>> observables.
>>
>>
>>
>>> This another question is regarding energy minimization. Suppose, I
>>> minimize the the protein solvated in water, the energy value that I get is
>>> for the whole system or for the protein alone. If it's for the system then
>>> how can I get the energy for the protein alone.
>>>
>>
>>  You can define energy groups (see manual) to do this for the nonbonded
>> contributions. Bonded contributions are easy to do in your case. Whether
>> this energy is useful for anything is quite another matter.
>>
>> Mark
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
>
>  --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
>
>
>
>
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
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Re: [gmx-users] Re: Dihedral Constraints


On 14/06/2012 4:38 PM, bharat gupta wrote:
Thanks Sir for the reply... This question is related to my first query 
that if we constraint the dihedral of the turn residue how can we 
fix/freeze the movement of other residues.


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

As I am interested in only getting the energy of the hairpin when the 
turn residues are constrained within a particular phi psi angle range


.. and with what are you going to compare those energies? And what will 
that comparison mean?


Mark




On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 14/06/2012 12:04 PM, bharat gupta wrote:

Thanks for the reply . Is it possible to calculate the
dihedral energy of certain residues, like in my case for turn
residues ??.. How can that be done


First, seek to define "dihedral energy"... Force fields are not
parametrized such that parts of them are expected to correlate
with observables.



This another question is regarding energy minimization.
Suppose, I minimize the the protein solvated in water, the
energy value that I get is for the whole system or for the
protein alone. If it's for the system then how can I get the
energy for the protein alone.


You can define energy groups (see manual) to do this for the
nonbonded contributions. Bonded contributions are easy to do in
your case. Whether this energy is useful for anything is quite
another matter.

Mark

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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 





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[gmx-users] Insertion protein in the membrane via G_membed

2012-06-13 Thread James Starlight

Dear Gromacs Users!

I've forced with the problem durin insertion of my protein into
pre-equilibrated bilayer via G_Membed.

I've done all steps in accordance to the KALP tutorial ( I've oriented both
membrane as well as the protein in the same dimensions merged both
topologies and gro files in the merged.gro file ) but after processed via
grompp I've recieved warning

WARNING 1 [file gmembed.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups


if I scip this message by maxwarn oprtins, g_membed remove only 10 lipids (
while > 40 are overlapped with the protein ) and during further g_membed's
md_run I've obtained lincs warning and my system is crushed .


I'm using berger lipids and that mdp file for the G_membed

integrator = md
energygrps  = Protein
freezegrps = Protein
freezedim  = Y Y Y
energygrp_table
energygrp_excl = Protein Protein



emtol= 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform

; Bond parameters
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
nstlist= 5; 10 fs
rlist= 1.2; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
rvdw= 1.2; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
pbc= xyz; 3-D PBC


Could you tell me where is the problem in my case might be?


James
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Re: [gmx-users] Re: Dihedral Constraints

Thanks Sir for the reply... This question is related to my first query that
if we constraint the dihedral of the turn residue how can we fix/freeze the
movement of other residues. As I am interested in only getting the energy
of the hairpin when the turn residues are constrained within a particular
phi psi angle range


On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham wrote:

> On 14/06/2012 12:04 PM, bharat gupta wrote:
>
>> Thanks for the reply . Is it possible to calculate the dihedral energy of
>> certain residues, like in my case for turn residues ??.. How can that be
>> done
>>
>
> First, seek to define "dihedral energy"... Force fields are not
> parametrized such that parts of them are expected to correlate with
> observables.
>
>
>
>> This another question is regarding energy minimization. Suppose, I
>> minimize the the protein solvated in water, the energy value that I get is
>> for the whole system or for the protein alone. If it's for the system then
>> how can I get the energy for the protein alone.
>>
>
> You can define energy groups (see manual) to do this for the nonbonded
> contributions. Bonded contributions are easy to do in your case. Whether
> this energy is useful for anything is quite another 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/Searchbefore
>  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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] g_lie reproducibility (g_lie is lying)


On 14/06/2012 3:56 PM, Tom Dupree wrote:

Greetings all,
I can't manually reproduce g_lie results.
After raging at excel for a while I think I have found a bug.

Here is my first time point,
Reported by g_lie to be 35.0073
> From energy file
Lj_complex =-130.762
Coul_complex = -286.746
My constants specified to g_lie
Clj = Alpha = lj_const = 0.181
Cqq = Beta = coul_const = 0.43
Elj = Lj_solv = -166
Eqq = Coul_solv = -263

Therefore
Lj_diff = 35.238
Coul_diff = -23.746

Hence
Lj_diff x lj_const = 6.378
Coul_diff x coul_const = -10.211

And there is no way I can add those to get 35.0073

However I can get this value using the following
Coul_complex - lj_solv = -120.746
Lj_complex - coul_solv = 132.2378
-120.746 x lj_const = -120.746 x 0.181 = -21.855
132.2378 x coul_const = 56.86225
Sum = 35.00726

In short I think the g_lie calculation has swapped its variables, Elj instead 
of Eqq and vice versa.


I think it's rather more likely you've made a transcription error going 
to Excel. You can check the code of src/tools/gmx_lie.c for exactly this 
kind of purpose, but I can't see any problem with it.




One other thing I have noticed is that when calculating the average g_lie uses 
the final value twice, is there a reason for this?

e.g.

  994 24.9397
  996 43.3382
  998 40.5714
1000 40.5585
1000 40.5585



Inspect your energy file with gmxdump - I think you've managed to 
duplicate the final frame at an earlier point of your workflow. eneconv 
has options to prevent such duplicates occuring during concatenation, 
etc. In any case, g_lie just eats what you give it...


Mark
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[gmx-users] g_lie reproducibility (g_lie is lying)

2012-06-13 Thread Tom Dupree

Greetings all,
I can't manually reproduce g_lie results.
After raging at excel for a while I think I have found a bug.

Here is my first time point,
Reported by g_lie to be 35.0073
>From energy file
Lj_complex =-130.762
Coul_complex = -286.746
My constants specified to g_lie
Clj = Alpha = lj_const = 0.181 
Cqq = Beta = coul_const = 0.43
Elj = Lj_solv = -166
Eqq = Coul_solv = -263

Therefore
Lj_diff = 35.238
Coul_diff = -23.746

Hence 
Lj_diff x lj_const = 6.378
Coul_diff x coul_const = -10.211

And there is no way I can add those to get 35.0073

However I can get this value using the following
Coul_complex - lj_solv = -120.746
Lj_complex - coul_solv = 132.2378
-120.746 x lj_const = -120.746 x 0.181 = -21.855
132.2378 x coul_const = 56.86225
Sum = 35.00726

In short I think the g_lie calculation has swapped its variables, Elj instead 
of Eqq and vice versa.
 
One other thing I have noticed is that when calculating the average g_lie uses 
the final value twice, is there a reason for this?

e.g.

 994 24.9397
 996 43.3382
 998 40.5714
1000 40.5585
1000 40.5585

All the best,
Tom

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Re: [gmx-users] Re: Dihedral Constraints


On 14/06/2012 12:04 PM, bharat gupta wrote:
Thanks for the reply . Is it possible to calculate the dihedral energy 
of certain residues, like in my case for turn residues ??.. How can 
that be done


First, seek to define "dihedral energy"... Force fields are not 
parametrized such that parts of them are expected to correlate with 
observables.




This another question is regarding energy minimization. Suppose, I 
minimize the the protein solvated in water, the energy value that I 
get is for the whole system or for the protein alone. If it's for the 
system then how can I get the energy for the protein alone.


You can define energy groups (see manual) to do this for the nonbonded 
contributions. Bonded contributions are easy to do in your case. Whether 
this energy is useful for anything is quite another matter.


Mark
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Re: [gmx-users] Re: Dihedral Constraints

Thanks for the reply . Is it possible to calculate the dihedral energy of
certain residues, like in my case for turn residues ??.. How can that be
done

This another question is regarding energy minimization. Suppose, I minimize
the the protein solvated in water, the energy value that I get is for the
whole system or for the protein alone. If it's for the system then how can
I get the energy for the protein alone.

On Thu, Jun 14, 2012 at 10:48 AM, Justin A. Lemkul  wrote:

>
>
> On 6/13/12 9:44 PM, bharat gupta wrote:
>
>> Hi,
>>
>> I wanted to simulate a beta-hairpin but with the dihedral angle of the
>> turn
>> residues constrained as per my wish for eg phi angle should not 60 and psi
>> should be 90. Can anybody tell me how can I do this ??
>>
>>
> http://www.gromacs.org/**Documentation/How-tos/**Dihedral_Restraints
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
>
> --
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>  posting!
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>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] unable to access redmine


On 14/06/2012 11:42 AM, Christopher Neale wrote:

Dear users:

the gromacs web page directs me to http://redmine.gromacs.org/ to file 
bug notifications.

The site, however, gives me a "500 internal server error".

Do I have the correct address?


Yes. It's down, and does so periodically.

Mark
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Re: [gmx-users] Re: Dihedral Constraints




On 6/13/12 9:44 PM, bharat gupta wrote:

Hi,

I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??



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

-Justin

--


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




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Re: [gmx-users] unable to access redmine




On 6/13/12 9:42 PM, Christopher Neale wrote:

Dear users:

the gromacs web page directs me to http://redmine.gromacs.org/ to file bug
notifications.
The site, however, gives me a "500 internal server error".

Do I have the correct address?



That is the correct address.  The page was down earlier, and apparently still 
is.

I'm CC'ing this to Rossen in case he's not reading gmx-users.

-Justin

--


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




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[gmx-users] Re: Dihedral Constraints

Hi,

I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??


Regards

-- 
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[gmx-users] unable to access redmine

2012-06-13 Thread Christopher Neale

Dear users:

the gromacs web page directs me to http://redmine.gromacs.org/ to file bug 
notifications.
The site, however, gives me a "500 internal server error".

Do I have the correct address?

Thank you,
Chris.
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Re: [gmx-users] Effect of vdwradii.dat


On 14/06/2012 2:31 AM, Anna Duncan wrote:


Hello all,

I'm doing a membrane-protein simulation using MARTINI of the ADP/ATP 
carrier in a POPC/POPE membrane.  After inserting the protein into the 
membrane I solvated the system using  g_genbox.  In order to prevent 
water beads from being placed within the bilayer, I made a local copy 
of vdwradii.dat with large vdw radii listed for acyl chain beads, as 
suggested in Justin Lemkul's useful membrane protein tutorial.


However, I forgot to delete the local copy of vdwradii.dat before 
moving on to further stages (ie. energy minimisation, equilibration 
and the final run).  Will this make a difference or is the information 
in vdwradii.dat only used for commands such as g_genbox and g_sas?  Is 
there any way of checking this?


I expect there is no difference. You can prove this by re-making your 
.tpr with a normal vdwradii.dat present and comparing both .tpr files 
with gmxcheck. mdrun uses only things on its command line as inputs.


Mark
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[gmx-users] Effect of vdwradii.dat

2012-06-13 Thread Anna Duncan



Hello all,

I'm doing a membrane-protein simulation using MARTINI of the ADP/ATP  
carrier in a POPC/POPE membrane.  After inserting the protein into the  
membrane I solvated the system using  g_genbox.  In order to prevent  
water beads from being placed within the bilayer, I made a local copy  
of vdwradii.dat with large vdw radii listed for acyl chain beads, as  
suggested in Justin Lemkul's useful membrane protein tutorial.


However, I forgot to delete the local copy of vdwradii.dat before  
moving on to further stages (ie. energy minimisation, equilibration  
and the final run).  Will this make a difference or is the information  
in vdwradii.dat only used for commands such as g_genbox and g_sas?  Is  
there any way of checking this?


Thanks,

Anna
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Re: [gmx-users] Error in production run

Hi Justin,

Thanks. I will have a look at this link.

On Thu, Jun 14, 2012 at 12:27 AM, Justin A. Lemkul  wrote:

>
>
> On 6/13/12 12:21 PM, Malai wrote:
>
>> Hi,
>>
>> Can you suggest me what went wrong in my production run . I got the
>> following
>> error that stopped my run. Thanks.
>>
>>
> http://www.gromacs.org/**Documentation/Terminology/**Blowing_Up
>
> -Justin
>
>
>  --**-
>> Program mdrun_mpi, VERSION 4.5.4
>> Source code file: domdec.c, line: 2861
>>
>> Fatal error:
>> The X-size of the box (6.311743) times the triclinic skew factor
>> (1.00) is
>> smaller than the number of DD cells (6) times the smallest allowed cell
>> size
>> (1.051861)
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> --**-
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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/Searchbefore
>  posting!
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>
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Re: [gmx-users] Error in production run




On 6/13/12 12:21 PM, Malai wrote:

Hi,

Can you suggest me what went wrong in my production run . I got the following
error that stopped my run. Thanks.



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

-Justin


---
Program mdrun_mpi, VERSION 4.5.4
Source code file: domdec.c, line: 2861

Fatal error:
The X-size of the box (6.311743) times the triclinic skew factor (1.00) is
smaller than the number of DD cells (6) times the smallest allowed cell size
(1.051861)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---




--


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




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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation




On 6/13/12 11:49 AM, ms wrote:

On 13/06/12 16:59, Justin A. Lemkul wrote:



On 6/13/12 10:48 AM, ms wrote:

On 13/06/12 16:36, Justin A. Lemkul wrote:

Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.


This is interesting -I have to ask the guys who devised the group's
standard
procedure :)


mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr



As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)

mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU

That's all you need.


 that's why -deffn it didn't work! silly me. Thanks!


I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)



I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.

>

Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)


Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying
to get the
system working on CPU and to see how it behaved before diving in the
GPU misty
sea...



Ah, sorry - with everything being named "GPU" it threw me off. I guess I
should have known based on the energy terms. When running on GPU, very
little information is printed (something I've complained about before) -
you only get Potential, Kinetic, Total, Temperature, and anything
related to constraints. I think it's due to limitations in OpenMM, not
Gromacs (something that should be improved in upcoming versions).

A few things to look at based on the .mdp file:

1. No constraints? Even with a 1-fs timestep, you probably need to be
constraining all least the h-bonds.


Ok. We usually don't constrain with 1-fs timestep, and since the gmx website
said that most restrains were unsupported, I didn't feel like adding them. Will
ask about this here.



Constraints and restraints are different.  Restraints are not supported. 
Constraints are, but not methods like LINCS.  OpenMM uses SHAKE/SETTLE/CCMA 
algorithms for constraints on GPU.



2. nstlist set to 2 is not going to give wrong results, but it's
incredibly time-consuming to do neighbor searching that often. A value
of 5 or 10 is probably more appropriate.


I have to ask why we use this value as default, and thanks for the tip -however
this seems not relevant now :)


3. COM removal of multiple groups can lead to bad energy conservation.


OK, good to know.


4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.


I am unsure of what do you mean. On the gmx website it reads:
"Temperature control: Supported only with the sd/sd1, bd, md/md-vv/md-vv-avek
integrators. OpenMM implements only the Andersen thermostat. All values for
tcoupl are thus accepted and equivalent to andersen. Multiple temperature
coupling groups are not supported, only tc-grps=System will work."

So it seems that *every* choice of mine means "andersen" in that context. Am I
wrong?


Huh, I guess this option is accepted.  What was unclear to me was that grompp 
would accept "Andersen" as a valid setting for tcoupl.  All that's being 
referenced in the quote above is that, no matter what you set for the tcoupl 
parameter, mdrun is going to use an Andersen thermostat.


-Justin




5. Why not use dispersion correction?


True, why not? :)
Will give it a shot.


thanks!
m.



--


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




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[gmx-users] Error in production run

Hi,

Can you suggest me what went wrong in my production run . I got the
following error that stopped my run. Thanks.

---
Program mdrun_mpi, VERSION 4.5.4
Source code file: domdec.c, line: 2861

Fatal error:
The X-size of the box (6.311743) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.051861)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
-- 
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!
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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation


On 13/06/12 16:59, Justin A. Lemkul wrote:



On 6/13/12 10:48 AM, ms wrote:

On 13/06/12 16:36, Justin A. Lemkul wrote:

Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.


This is interesting -I have to ask the guys who devised the group's
standard
procedure :)


mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr



As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)

mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU

That's all you need.


 that's why -deffn it didn't work! silly me. Thanks!


I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)



I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.

>

Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)


Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying
to get the
system working on CPU and to see how it behaved before diving in the
GPU misty
sea...



Ah, sorry - with everything being named "GPU" it threw me off. I guess I
should have known based on the energy terms. When running on GPU, very
little information is printed (something I've complained about before) -
you only get Potential, Kinetic, Total, Temperature, and anything
related to constraints. I think it's due to limitations in OpenMM, not
Gromacs (something that should be improved in upcoming versions).

A few things to look at based on the .mdp file:

1. No constraints? Even with a 1-fs timestep, you probably need to be
constraining all least the h-bonds.


Ok. We usually don't constrain with 1-fs timestep, and since the gmx 
website said that most restrains were unsupported, I didn't feel like 
adding them. Will ask about this here.



2. nstlist set to 2 is not going to give wrong results, but it's
incredibly time-consuming to do neighbor searching that often. A value
of 5 or 10 is probably more appropriate.


I have to ask why we use this value as default, and thanks for the tip 
-however this seems not relevant now :)



3. COM removal of multiple groups can lead to bad energy conservation.


OK, good to know.


4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.


I am unsure of what do you mean. On the gmx website it reads:
"Temperature control: Supported only with the sd/sd1, bd, 
md/md-vv/md-vv-avek integrators. OpenMM implements only the Andersen 
thermostat. All values for tcoupl are thus accepted and equivalent to 
andersen. Multiple temperature coupling groups are not supported, only 
tc-grps=System will work."


So it seems that *every* choice of mine means "andersen" in that 
context. Am I wrong?



5. Why not use dispersion correction?


True, why not? :)
Will give it a shot.


thanks!
m.

--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at 
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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation




On 6/13/12 10:48 AM, ms wrote:

On 13/06/12 16:36, Justin A. Lemkul wrote:

Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.


This is interesting -I have to ask the guys who devised the group's standard
procedure :)


mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr



As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)

mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU

That's all you need.


 that's why -deffn it didn't work! silly me. Thanks!


I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)



I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.

 >

Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)


Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying to get the
system working on CPU and to see how it behaved before diving in the GPU misty
sea...



Ah, sorry - with everything being named "GPU" it threw me off.  I guess I should 
have known based on the energy terms.  When running on GPU, very little 
information is printed (something I've complained about before) - you only get 
Potential, Kinetic, Total, Temperature, and anything related to constraints.  I 
think it's due to limitations in OpenMM, not Gromacs (something that should be 
improved in upcoming versions).


A few things to look at based on the .mdp file:

1. No constraints?  Even with a 1-fs timestep, you probably need to be 
constraining all least the h-bonds.


2. nstlist set to 2 is not going to give wrong results, but it's incredibly 
time-consuming to do neighbor searching that often.  A value of 5 or 10 is 
probably more appropriate.


3. COM removal of multiple groups can lead to bad energy conservation.

4. What happens when you use the Andersen thermostat?  That's not implemented 
yet for CPU calculations (though it was recently pushed into the 4.6 development 
branch).  Your comment regarding GPU is fine, but I would think grompp would 
complain.


5. Why not use dispersion correction?

-Justin

--


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




--
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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 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation


On 13/06/12 16:36, Justin A. Lemkul wrote:

Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.


This is interesting -I have to ask the guys who devised the group's 
standard procedure :)



mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr



As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)

mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU

That's all you need.


 that's why -deffn it didn't work! silly me. Thanks!


I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)



I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.

>

Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)


Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying to 
get the system working on CPU and to see how it behaved before diving in 
the GPU misty sea...


thanks,
Massimo

--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
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 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

On 6/13/12 10:20 AM, ms wrote:

Hi,

I am trying to prepare a simple system for tests with CUDA. My guinea pig is the
lysozyme system from this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html

but I prepared it using the AMBER99sb-ildn force field and the SPCE water model.

After extensive minimization steps, I started a (CPU) very short test run (3 ns)
to check if everything was ok before beginning to deal with CUDA.

However I found that there is a strong drift in energy and temperature:

 >g_energy_d output:

  Opened 1AKI_production_GPU.edr as double precision energy file

  Select the terms you want from the following list by
  selecting either (part of) the name or the number or a combination.
  End your selection with an empty line or a zero.
  ---
1  Bond 2  Angle3  Proper-Dih.  4 Improper-Dih.
5  LJ-146  Coulomb-14   7  LJ-(SR)  8 Coulomb-(SR)
9  Coul.-recip.10  Potential   11  Kinetic-En. 12 Total- Energy
   13  Temperature 14  Pressure15  Box-X   16 Box-Y
   17  Box-Z   18  Volume  19  Density 20  pV
   21  Enthalpy22  Vir-XX  23  Vir-XY  24 Vir-XZ
   25  Vir-YX  26  Vir-YY  27  Vir-YZ  28 Vir-ZX
   29  Vir-ZY  30  Vir-ZZ  31  Pres-XX 32 Pres-XY
   33  Pres-XZ 34  Pres-YX 35  Pres-YY 36 Pres-YZ
   37  Pres-ZX 38  Pres-ZY 39  Pres-ZZ 40 #Surf*SurfTen
   41  Box-Vel-XX  42  Box-Vel-YY  43  Box-Vel-ZZ  44  Mu-X
   45  Mu-Y46  Mu-Z
   47  Coul-SR:Protein-Protein 48  LJ-SR:Protein-Protein
   49  Coul-14:Protein-Protein 50  LJ-14:Protein-Protein
   51  Coul-SR:Protein-non-Protein 52  LJ-SR:Protein-non-Protein
   53  Coul-14:Protein-non-Protein 54  LJ-14:Protein-non-Protein
   55  Coul-SR:non-Protein-non-Protein 56 LJ-SR:non-Protein-non-Protein
   57  Coul-14:non-Protein-non-Protein 58 LJ-14:non-Protein-non-Protein
   59  T-System

10
11
12
13
14

  Last energy frame read 3 time 5000.000

  Statistics over 301 steps [ 2000. through 5000. ps ], 5 data sets
  All statistics are over 151 points

  Energy  Average   Err.Est.   RMSD  Tot-Drift

---
  Potential   -529618   15003004.68   -10322.5  (kJ/mol)
  Kinetic En. 86141.8610 1295.7   -4294.67 (kJ/mol)
  Total Energy-443476   21004220.26   -14617.1 (kJ/mol)
  Temperature  292.492.14.39949   -14.5823   (K)
  Pressure1.02119 0.0046133.601 -0.0134421 (bar)

  You may want to use the -driftcorr flag in order to correct
  for spurious drift in the graphs. Note that this is not
  a substitute for proper equilibration and sampling!

  WARNING: nmol = 1, this may not be what you want.

Temperature dependent fluctuation properties at T = 292.49.

The MDP is:

 >production_GPU.mdp

; PREPROCESSING OPTIONS
title= production run 1 for GPU usage
include=
define=
; RUN CONTROL PARAMETERS
integrator= md; for GPUs: "Option md is accepted but keep in
mind that the actual algorithm is not leap-frog."

tinit= 2000
dt= 0.001; 1 fs
nsteps= 300; 3 ns
init_step= 0
; CENTER OF MASS MOTION REMOVAL
nstcomm= 1
comm_mode= linear
comm_grps= protein non-protein
; OUTPUT CONTROL
nstxout= 2000; Doubled these because disk output is a strong
bottleneck apparently

nstvout= 2000
nstfout= 0
nstlog= 100
nstenergy= 100
nstxtcout= 100
nstcalcenergy   = -1
xtcprecision= 1000
energygrps= protein non-protein
; NEIGHBOR SEARCHING PARAMETERS
nstlist= 2.
ns_type= grid
pbc= xyz
rlist= 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype= PME; this is OK for GPUs
rcoulomb_switch= 0.
rcoulomb= 1.0
epsilon_r= 1
vdwtype= cut-off
rvdw-switch= 0.
rvdw= 1.0
DispCorr= no
fourierspacing= 0.12
fourier_nx= 0
fourier_ny= 0
fourier_nz= 0
pme_order= 4
ewald_rtol= 1e-05
epsilon_surface= 0
optimize_fft= no
; TEMPERATURE COUPLING
tcoupl= andersen; All values of this are equivalent to
"andersen" in GPU mode
tc_grps= system
tau_t= 0.1
ref_t= 300.00
; PRESSURE COUPLING
pcoupl= parrinello-rahman; "OpenMM implements the Monte Car

[gmx-users] Re: Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

Looking deeper, it seems most of the energy loss is concentrated in the 
SR Coulomb interactions:


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Bond2771.28 1792.5698   -120.382 
(kJ/mol)
Angle3796.4 25106.584   -169.737 
(kJ/mol)
Proper Dih. 5106.24 1054.0963   -66.3269 
(kJ/mol)
Improper Dih.   261.4211.721.1174   -11.8454 
(kJ/mol)
LJ-14   1865.58   0.5936.7259   -2.92646 
(kJ/mol)
Coulomb-1416174 14  118.8   -58.9593 
(kJ/mol)
LJ (SR) 94061.95601333.143958.04 
(kJ/mol)
Coulomb (SR)-578731   19004045.78   -13704.5 
(kJ/mol)
Coul. recip.   -74923.8 2381.0255   -145.854 
(kJ/mol)
Potential   -529618   15003004.68   -10322.5 
(kJ/mol)
Kinetic En. 86141.8610 1295.7   -4294.67 
(kJ/mol)
Total Energy-443476   21004220.26   -14617.1 
(kJ/mol)

Temperature  292.492.14.39949   -14.5823  (K)
Pressure1.02119 0.0046133.601 -0.0134421  (bar)
Volume  343.801   0.32   0.955516-2.2844  (nm^3)
Density 1012.34   0.942.813496.72636 
(kg/m^3)




Also, the drift is almost perfectly linear (apart from the noise).


--
Massimo Sandal, Ph.D.
http://devicerandom.org
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[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation


Hi,

I am trying to prepare a simple system for tests with CUDA. My guinea 
pig is the lysozyme system from this tutorial: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html


but I prepared it using the AMBER99sb-ildn force field and the SPCE 
water model.


After extensive minimization steps, I started a (CPU) very short test 
run (3 ns) to check if everything was ok before beginning to deal with CUDA.


However I found that there is a strong drift in energy and temperature:

>g_energy_d output:

 Opened 1AKI_production_GPU.edr as double precision energy file

 Select the terms you want from the following list by
 selecting either (part of) the name or the number or a combination.
 End your selection with an empty line or a zero.
 ---
   1  Bond 2  Angle3  Proper-Dih.  4 
Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8 
Coulomb-(SR)
   9  Coul.-recip.10  Potential   11  Kinetic-En. 12 
Total- Energy
  13  Temperature 14  Pressure15  Box-X   16 
Box-Y
  17  Box-Z   18  Volume  19  Density 20  pV 

  21  Enthalpy22  Vir-XX  23  Vir-XY  24 
Vir-XZ
  25  Vir-YX  26  Vir-YY  27  Vir-YZ  28 
Vir-ZX
  29  Vir-ZY  30  Vir-ZZ  31  Pres-XX 32 
Pres-XY
  33  Pres-XZ 34  Pres-YX 35  Pres-YY 36 
Pres-YZ
  37  Pres-ZX 38  Pres-ZY 39  Pres-ZZ 40 
#Surf*SurfTen
  41  Box-Vel-XX  42  Box-Vel-YY  43  Box-Vel-ZZ  44  Mu-X 

  45  Mu-Y46  Mu-Z 

  47  Coul-SR:Protein-Protein 48  LJ-SR:Protein-Protein 

  49  Coul-14:Protein-Protein 50  LJ-14:Protein-Protein 

  51  Coul-SR:Protein-non-Protein 52  LJ-SR:Protein-non-Protein 

  53  Coul-14:Protein-non-Protein 54  LJ-14:Protein-non-Protein 

  55  Coul-SR:non-Protein-non-Protein 56 
LJ-SR:non-Protein-non-Protein
  57  Coul-14:non-Protein-non-Protein 58 
LJ-14:non-Protein-non-Protein

  59  T-System

10
11
12
13
14

 Last energy frame read 3 time 5000.000

 Statistics over 301 steps [ 2000. through 5000. ps ], 5 
data sets

 All statistics are over 151 points

 Energy  Average   Err.Est.   RMSD  Tot-Drift

---
 Potential   -529618   15003004.68   -10322.5 
 (kJ/mol)
 Kinetic En. 86141.8610 1295.7   -4294.67 
(kJ/mol)
 Total Energy-443476   21004220.26   -14617.1 
(kJ/mol)

 Temperature  292.492.14.39949   -14.5823   (K)
 Pressure1.02119 0.0046133.601 -0.0134421 
(bar)


 You may want to use the -driftcorr flag in order to correct
 for spurious drift in the graphs. Note that this is not
 a substitute for proper equilibration and sampling!

 WARNING: nmol = 1, this may not be what you want.

Temperature dependent fluctuation properties at T = 292.49.


The MDP is:

>production_GPU.mdp

; PREPROCESSING OPTIONS
title   = production run 1 for GPU usage
include =
define  =
; RUN CONTROL PARAMETERS
integrator		= md		; for GPUs: "Option md is accepted but keep in mind 
that the actual algorithm is not leap-frog."


tinit   = 2000
dt  = 0.001 ; 1 fs
nsteps  = 300   ; 3 ns
init_step   = 0
; CENTER OF MASS MOTION REMOVAL
nstcomm = 1
comm_mode   = linear
comm_grps   = protein non-protein
; OUTPUT CONTROL
nstxout			= 2000		; Doubled these because disk output is a strong 
bottleneck apparently


nstvout = 2000
nstfout = 0
nstlog  = 100
nstenergy   = 100
nstxtcout   = 100
nstcalcenergy   = -1
xtcprecision= 1000
energygrps  = protein non-protein
; NEIGHBOR SEARCHING PARAMETERS
nstlist = 2.
ns_type = grid
pbc = xyz
rlist   = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME   ; this is OK for GPUs
rcoulomb_switch = 0.
rcoulomb= 1.0
epsilon_r   = 1
vdwtype = cut-off
rvdw-switch = 0.
rvdw= 1.0
DispCorr= no
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-05
epsilon_surface = 0
optimize_fft= no
; TEMPERATURE COUPLING
tcoupl			= andersen	; All values of this are equivalent to "andersen" in 
GPU mode

tc_grps

Re: [gmx-users] input/output error in production grompp

On 6/13/12 9:22 AM, Malai wrote:

HI Justin,

I did use the .pdb file as I showed in the grompp command. If I got I/O error,
the mdrun should not work? but here the mdrun is working. Thanks.

As I said before, if the .tpr file was produced, there was no problem.  The 
error message makes no sense at all to me.

-Justin

On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:

On 6/13/12 9:11 AM, Malai wrote:

Hello Justin,

Thanks for reply. After getting this, I started to run production run
but here i
didnt get any error. so is it OK? or still I need to look at this error?
Thanks

What's anomalous to me is that grompp produced an I/O error (referencing an
unused or nonexistent file) but still produced a .tpr file.  Fatal errors
prevent grompp from working, so you shouldn't have gotten a .tpr file in
this case.

You need coordinates in the .tpr file to work, but if you did in fact use a
.pdb file, then the .tpr is fine.  The reference to the .gro file is still a
complete mystery to me.

-Justin

On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul mailto:jalem...@vt.edu>
>> wrote:

On 6/13/12 8:27 AM, Malai wrote:

HI,

Sorry for wrongly typing. The command I issued is:  grompp -v -f
hex1.mdp -c
hex1.pdb -p hex1.top -o hex1.tpr.

The error is bellow:

Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491

File input/output error:
hex1.gro
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/__Documentation/Errors

>

>>

Even with the corrected command, I see no way for this error to 
come up.
  There is no reference to a .gro file anywhere in your command.

-Justin

--
====

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu   | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

>

====

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080 

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Re: [gmx-users] input/output error in production grompp

HI Justin,

I did use the .pdb file as I showed in the grompp command. If I got I/O
error, the mdrun should not work? but here the mdrun is working. Thanks.

On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul  wrote:

>
>
> On 6/13/12 9:11 AM, Malai wrote:
>
>> Hello Justin,
>>
>> Thanks for reply. After getting this, I started to run production run but
>> here i
>> didnt get any error. so is it OK? or still I need to look at this error?
>> Thanks
>>
>>
> What's anomalous to me is that grompp produced an I/O error (referencing
> an unused or nonexistent file) but still produced a .tpr file.  Fatal
> errors prevent grompp from working, so you shouldn't have gotten a .tpr
> file in this case.
>
> You need coordinates in the .tpr file to work, but if you did in fact use
> a .pdb file, then the .tpr is fine.  The reference to the .gro file is
> still a complete mystery to me.
>
> -Justin
>
>  On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul > > wrote:
>>
>>
>>
>>On 6/13/12 8:27 AM, Malai wrote:
>>
>>HI,
>>
>>Sorry for wrongly typing. The command I issued is:  grompp -v -f
>> hex1.mdp -c
>>hex1.pdb -p hex1.top -o hex1.tpr.
>>
>>The error is bellow:
>>
>>
>>Error:
>>Program grompp, VERSION 4.5.4
>>Source code file: futil.c, line: 491
>>
>>File input/output error:
>>hex1.gro
>>For more information and tips for troubleshooting, please check
>> the GROMACS
>>website at 
>> http://www.gromacs.org/**Documentation/Errors
>>
>> 
>> >
>>
>>
>> 
>>
>> 
>> >>
>>
>>
>>Even with the corrected command, I see no way for this error to come
>> up.
>>  There is no reference to a .gro file anywhere in your command.
>>
>>
>>-Justin
>>
>>--
>>==**__==
>>
>>
>>Justin A. Lemkul, Ph.D.
>>Research Scientist
>>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 list gmx-users@gromacs.org > gmx-users@gromacs.org>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>>
>> 
>> >
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>>
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>>
>>
>> >
>> before posting!
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>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
>
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C

Re: [gmx-users] input/output error in production grompp




On 6/13/12 9:11 AM, Malai wrote:

Hello Justin,

Thanks for reply. After getting this, I started to run production run but here i
didnt get any error. so is it OK? or still I need to look at this error? Thanks



What's anomalous to me is that grompp produced an I/O error (referencing an 
unused or nonexistent file) but still produced a .tpr file.  Fatal errors 
prevent grompp from working, so you shouldn't have gotten a .tpr file in this 
case.


You need coordinates in the .tpr file to work, but if you did in fact use a .pdb 
file, then the .tpr is fine.  The reference to the .gro file is still a complete 
mystery to me.


-Justin


On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



On 6/13/12 8:27 AM, Malai wrote:

HI,

Sorry for wrongly typing. The command I issued is:  grompp -v -f 
hex1.mdp -c
hex1.pdb -p hex1.top -o hex1.tpr.

The error is bellow:


Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491

File input/output error:
hex1.gro
For more information and tips for troubleshooting, please check the 
GROMACS
website at http://www.gromacs.org/Documentation/Errors

>


Even with the corrected command, I see no way for this error to come up.
  There is no reference to a .gro file anywhere in your command.


-Justin

--
==__==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080 

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==


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--


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




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Re: [gmx-users] input/output error in production grompp

Hello Justin,

Thanks for reply. After getting this, I started to run production run but
here i didnt get any error. so is it OK? or still I need to look at this
error? Thanks

On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul  wrote:

>
>
> On 6/13/12 8:27 AM, Malai wrote:
>
>> HI,
>>
>> Sorry for wrongly typing. The command I issued is:  grompp -v -f hex1.mdp
>> -c
>> hex1.pdb -p hex1.top -o hex1.tpr.
>>
>> The error is bellow:
>>
>>
>> Error:
>> Program grompp, VERSION 4.5.4
>> Source code file: futil.c, line: 491
>>
>> File input/output error:
>> hex1.gro
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/__**Documentation/Errors
>> 
>> >
>>
>>
> Even with the corrected command, I see no way for this error to come up.
>  There is no reference to a .gro file anywhere in your command.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
>
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
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Re: [gmx-users] Errors in Minimization using grompp




On 6/13/12 8:59 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi Justin,
I managed it with your help that the minimization run worked. Now I
prepared a .mdp file for the md run.
Can you please tell me if the following .mdp file is correct?

define  = -DPOSRES
integrator  =  md
constraints =  all-bonds
emtol = 8
niter = 15


The preceding two lines are irrelevant.


nsteps  =  5


You haven't set a value for dt.  The default is 0.001 ps, but with all bonds 
constrained, you can set it to 0.002 for better performance.



nstlist =  1


Neighbor searching at every step is extremely time-consuming, and largely 
unnecessary.  For EM, nstlist must be set to 1, but for MD, it should not.  To 
invoke the optimized all-vs-all kernels (in conjunction with the other settings 
that trigger them), set nstlist=0 for a fixed neighbor list.


-Justin


ns_type =  simple
rlist   =  0
comm-mode   =  angular
comm-grps   =  System
coulombtype =  cut-off
vdwtype =  cut-off
rcoulomb=  0
rvdw=  0
pbc =  no
epsilon_rf  =  0
implicit_solvent=  GBSA
gb_algorithm=   HCT
nstgbradii  =  1
rgbradii=  0
gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm=  Ace-approximation
sa_surface_tension  = -1


Thank you,
Eva




On 6/13/12 7:55 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi!
Thank you for your answer.


On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:

Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.


Doesn't really matter - nothing will move more than a fraction of an
Angstrom unless it's horribly wrong, in which case not moving the heavy
atoms won't help you.


And I want to do this with implicit solvent.


Probably not worth the effort if you're just preparing for MD.


Our goal is not an MD simulation of the protein. We plan a
Poisson-Boltzmann electrostatics calculation. For that we need the heavy
atoms as they are in the crystal structure (even 1 Angstroem movement
would be too much) with good hydrogen atom position.


With restraints on heavy atoms, your positions will not deviate very much
at
all.  A 1 Angstrom movement would be huge in this case; I would expect
your
deviations to be orders of magnitude less.


We need to minimize, simulate, minimize, simulate the hydrogen atoms.


I don't follow the logic here.  You say you need to do an EM of the H
atoms in
order to do some PBSA calculation with no MD, but here you're doing two
iterations of EM and MD.


Implicit solvent is ok for us. (For a later MD run of the complete
protein, we will use explicit solvent).

This is the .mdp file:



There are several problems here, most of which I've already stated, but
I'll
recapitulate them again.



define  =  -DPOSRES
constraints =  all-bonds
integrator  =  steep
nsteps  =  3
vdwtype =  cutoff
coulombtype =  cutoff


As Mark said, these settings should be "cut-off" not "cutoff."


epsilon_rf = 0
pbc =  xyz


For an implicit system, periodicity should be set to "no" and grompp will
warn
you about using angular COM removal (invoked below) if you leave it set as
is.


nstlist =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.2
rvdw=  1.2


Finite cutoffs with implicit solvent will lead to instability and poor
energy
conservation.  These three lines (rlist, rcoulomb, rvdw) should be set to
zero,
unless you're satisfied with artifacts.


rvdw_switch = 0.7


This setting has no effect when using cutoffs.


comm-mode   =  angular
comm-grps   =  System
nstcgsteep = 1000
emtol   =  5.0


Unless you've compiled with double precision, it is unlikely you will
achieve a
minimal force this low.  The use of restraints is going to preclude most
movement in the system, so don't be surprised if grompp does not (and
cannot)
achieve this tolerance.


emstep  =  0.01
implicit_solvent=  GBSA
gb_algorithm=   HCT
nstgbradii  =  1
rgbradii=  1


This should also be set to zero if the above neighbor searching parameters
are zero.


gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm=  Ace-approximation
sa_surface_tension  = -1

Additionally I have a question according to the vdwtype and coulombtype.
Why do I have to set the two parameters to cutoff?



Because settings like PME don't make sense for implicit solvent
calculations.
Plain cutoffs with finite values are almost never adequate for any
purpose, however.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.beva

Re: [gmx-users] Errors in Minimization using grompp

Hi Justin,
I managed it with your help that the minimization run worked. Now I
prepared a .mdp file for the md run.
Can you please tell me if the following .mdp file is correct?

define  = -DPOSRES
integrator  =  md
constraints =  all-bonds
emtol = 8
niter = 15
nsteps  =  5
nstlist =  1
ns_type =  simple
rlist   =  0
comm-mode   =  angular
comm-grps   =  System
coulombtype =  cut-off
vdwtype =  cut-off
rcoulomb=  0
rvdw=  0
pbc =  no
epsilon_rf  =  0
implicit_solvent=  GBSA
gb_algorithm=   HCT
nstgbradii  =  1
rgbradii=  0
gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm=  Ace-approximation
sa_surface_tension  = -1


Thank you,
Eva


>
> On 6/13/12 7:55 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi!
>> Thank you for your answer.
>>
>>> On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de
>>> wrote:
 Hi everybody,
 I want to do a minimization of the hydrogens of my protein. Only the
 hydrogens.
>>>
>>> Doesn't really matter - nothing will move more than a fraction of an
>>> Angstrom unless it's horribly wrong, in which case not moving the heavy
>>> atoms won't help you.
>>>
And I want to do this with implicit solvent.
>>>
>>> Probably not worth the effort if you're just preparing for MD.
>>
>> Our goal is not an MD simulation of the protein. We plan a
>> Poisson-Boltzmann electrostatics calculation. For that we need the heavy
>> atoms as they are in the crystal structure (even 1 Angstroem movement
>> would be too much) with good hydrogen atom position.
>
> With restraints on heavy atoms, your positions will not deviate very much
> at
> all.  A 1 Angstrom movement would be huge in this case; I would expect
> your
> deviations to be orders of magnitude less.
>
>> We need to minimize, simulate, minimize, simulate the hydrogen atoms.
>
> I don't follow the logic here.  You say you need to do an EM of the H
> atoms in
> order to do some PBSA calculation with no MD, but here you're doing two
> iterations of EM and MD.
>
>> Implicit solvent is ok for us. (For a later MD run of the complete
>> protein, we will use explicit solvent).
>>
>> This is the .mdp file:
>>
>
> There are several problems here, most of which I've already stated, but
> I'll
> recapitulate them again.
>
>>
>> define  =  -DPOSRES
>> constraints =  all-bonds
>> integrator  =  steep
>> nsteps  =  3
>> vdwtype =  cutoff
>> coulombtype =  cutoff
>
> As Mark said, these settings should be "cut-off" not "cutoff."
>
>> epsilon_rf = 0
>> pbc =  xyz
>
> For an implicit system, periodicity should be set to "no" and grompp will
> warn
> you about using angular COM removal (invoked below) if you leave it set as
> is.
>
>> nstlist =  1
>> ns_type =  grid
>> rlist   =  1
>> rcoulomb=  1.2
>> rvdw=  1.2
>
> Finite cutoffs with implicit solvent will lead to instability and poor
> energy
> conservation.  These three lines (rlist, rcoulomb, rvdw) should be set to
> zero,
> unless you're satisfied with artifacts.
>
>> rvdw_switch = 0.7
>
> This setting has no effect when using cutoffs.
>
>> comm-mode   =  angular
>> comm-grps   =  System
>> nstcgsteep = 1000
>> emtol   =  5.0
>
> Unless you've compiled with double precision, it is unlikely you will
> achieve a
> minimal force this low.  The use of restraints is going to preclude most
> movement in the system, so don't be surprised if grompp does not (and
> cannot)
> achieve this tolerance.
>
>> emstep  =  0.01
>> implicit_solvent=  GBSA
>> gb_algorithm=   HCT
>> nstgbradii  =  1
>> rgbradii=  1
>
> This should also be set to zero if the above neighbor searching parameters
> are zero.
>
>> gb_epsilon_solvent  =  80
>> gb_saltconc   =  0
>> sa_algorithm=  Ace-approximation
>> sa_surface_tension  = -1
>>
>> Additionally I have a question according to the vdwtype and coulombtype.
>> Why do I have to set the two parameters to cutoff?
>>
>
> Because settings like PME don't make sense for implicit solvent
> calculations.
> Plain cutoffs with finite values are almost never adequate for any
> purpose, however.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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!
> P

Re: [gmx-users] GPU

2012-06-13 Thread Szilárd Páll

On Wed, Jun 13, 2012 at 3:59 AM, Mark Abraham wrote:

> On 12/06/2012 10:49 PM, Ehud Schreiber wrote:
>
>> Message: 4
>>> Date: Mon, 11 Jun 2012 15:54:39 +1000
>>> From: Mark Abraham>
>>> Subject: Re: [gmx-users] GPU
>>> To: Discussion list for GROMACS users
>>> Message-ID:<4FD5881F.3040509@**anu.edu.au <4fd5881f.3040...@anu.edu.au>>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> On 11/06/2012 2:32 AM, ifat shub wrote:
>>>
 Hi,



 If I understand correctly, currently the Gromacs GPU acceleration does
 not support energy minimization. Is this so? Are there any plans to
 include it in the 4.6 version or in a later one (i.e. to allow, say,
 integrator = steep or cg in mdrun-gpu)? I would find such options
 extremely useful.

>>> EM is normally so quick that it's not worth putting much effort into
>>> accelerating it, compared to the CPU-months that are spent doing
>>> subsequent MD.
>>>
>>> Mark
>>>
>> Currently, my main use of Gromacs entails running multiple minimizations
>> on an ensemble of states.
>> Moreover, these states are not obtained using molecular dynamics but
>> rather using the Concoord algorithm.
>> Therefore, for me the bottleneck is not md but rather minimizations
>> (specifically, cg) and so their acceleration on GPUs would be very
>> advantageous.
>> If such usage is not totally idiosyncratic, I hope the development team
>> would reconsider GPU accelerating also minimizations.
>> I suspect this would not be technically too complex given the work
>> already done on dynamics.
>>
>
> I suspect the upcoming 4.6 release will have GPU-accelerated EM available
> as a side effect of the new Verlet pair-list scheme for computing
> non-bonded interactions. This development is unrelated to previous GPU
> efforts, I


It does work and has been tested extensively. We are working on the final
details,  but you can get the code from the nbnxn_hybrid_acc branch -- it's
pretty safe to use it for non-production purposes!

The pages Mark linked are the resources you want to start with before you
start using the NxN kernels.

Cheers,
--
Szilárd


> understand. See http://www.gromacs.org/**Documentation/Acceleration_**
> and_parallelizationand
> http://www.gromacs.org/**Documentation/Cut-off_schemesfor
>  some advance details. When you hear a call for alpha testers in the
> next few

months, you might want to spend some time on that so that you're sure
> GROMACS will best meet your future needs. :-)



>
>
> Mark
>
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] input/output error in production grompp




On 6/13/12 8:27 AM, Malai wrote:

HI,

Sorry for wrongly typing. The command I issued is:  grompp -v -f hex1.mdp -c
hex1.pdb -p hex1.top -o hex1.tpr.

The error is bellow:


Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491

File input/output error:
hex1.gro
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/__Documentation/Errors




Even with the corrected command, I see no way for this error to come up.  There 
is no reference to a .gro file anywhere in your command.


-Justin

--


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




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Re: [gmx-users] unknown residue (BGC)




On 6/13/12 8:20 AM, delara aghaie wrote:

Dear Justin
If we do not get error when using command pdb2gmx, and so having the .top and
.gro files, Can we make sure that every thing is ok with our pdb file or maybe
there exists some other checks to be done on pdb?


If pdb2gmx produces no error, then the contents of the initial coordinate file 
matched the expectations of the force field and thus the topology and resulting 
structure are fine.


-Justin

--


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




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Re: [gmx-users] input/output error in production grompp

HI,

Sorry for wrongly typing. The command I issued is:  grompp  -v -f hex1.mdp
-c hex1.pdb -p hex1.top -o hex1.tpr.

The error is bellow:


Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491

File input/output error:
hex1.gro
For more information and tips for troubleshooting, please check the GROMACS
website at 
http://www.gromacs.org/**Documentation/Errors


Thanks.



On Wed, Jun 13, 2012 at 7:52 PM, Justin A. Lemkul  wrote:

>
>
> On 6/13/12 7:36 AM, Malai wrote:
>
>> Hi,
>>
>> I used the command following to generate .tpr file for production but I
>> got the
>> following error. Without considering this error, I run production but it
>> is
>> working now. any problem will be in production?
>>
>>
> The command below makes no sense; how is it that you were able to produce
> a .tpr file for your simulation?
>
>
>  -v -f hex1.mpb -c hex1.pdb -p hex1.top -o hex1.pdb
>>
>>
> This is not the command you typed (it contains several errors, both
> logical and typographical), and it certainly has nothing to do with the
> error below, as no reference is made to a file called "hex1.gro."  When
> reporting problems, please always copy and paste directly from your
> terminal.  Re-typing what you think you typed is error prone and wastes
> time.
>
>
>  Error:
>> Program grompp, VERSION 4.5.4
>> Source code file: futil.c, line: 491
>>
>> File input/output error:
>> hex1.gro
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>>
>>
> I/O errors occur when either a file isn't found in the working directory
> (i.e. doesn't exist) or can't be produced (insufficient permission or disk
> space to write the file).
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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/Searchbefore
>  posting!
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Re: [gmx-users] Errors in Minimization using grompp

Thank you very much for this quick answer!!
Eva

>
>
> On 6/13/12 7:55 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi!
>> Thank you for your answer.
>>
>>> On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de
>>> wrote:
 Hi everybody,
 I want to do a minimization of the hydrogens of my protein. Only the
 hydrogens.
>>>
>>> Doesn't really matter - nothing will move more than a fraction of an
>>> Angstrom unless it's horribly wrong, in which case not moving the heavy
>>> atoms won't help you.
>>>
And I want to do this with implicit solvent.
>>>
>>> Probably not worth the effort if you're just preparing for MD.
>>
>> Our goal is not an MD simulation of the protein. We plan a
>> Poisson-Boltzmann electrostatics calculation. For that we need the heavy
>> atoms as they are in the crystal structure (even 1 Angstroem movement
>> would be too much) with good hydrogen atom position.
>
> With restraints on heavy atoms, your positions will not deviate very much
> at
> all.  A 1 Angstrom movement would be huge in this case; I would expect
> your
> deviations to be orders of magnitude less.
>
>> We need to minimize, simulate, minimize, simulate the hydrogen atoms.
>
> I don't follow the logic here.  You say you need to do an EM of the H
> atoms in
> order to do some PBSA calculation with no MD, but here you're doing two
> iterations of EM and MD.
>
>> Implicit solvent is ok for us. (For a later MD run of the complete
>> protein, we will use explicit solvent).
>>
>> This is the .mdp file:
>>
>
> There are several problems here, most of which I've already stated, but
> I'll
> recapitulate them again.
>
>>
>> define  =  -DPOSRES
>> constraints =  all-bonds
>> integrator  =  steep
>> nsteps  =  3
>> vdwtype =  cutoff
>> coulombtype =  cutoff
>
> As Mark said, these settings should be "cut-off" not "cutoff."
>
>> epsilon_rf = 0
>> pbc =  xyz
>
> For an implicit system, periodicity should be set to "no" and grompp will
> warn
> you about using angular COM removal (invoked below) if you leave it set as
> is.
>
>> nstlist =  1
>> ns_type =  grid
>> rlist   =  1
>> rcoulomb=  1.2
>> rvdw=  1.2
>
> Finite cutoffs with implicit solvent will lead to instability and poor
> energy
> conservation.  These three lines (rlist, rcoulomb, rvdw) should be set to
> zero,
> unless you're satisfied with artifacts.
>
>> rvdw_switch = 0.7
>
> This setting has no effect when using cutoffs.
>
>> comm-mode   =  angular
>> comm-grps   =  System
>> nstcgsteep = 1000
>> emtol   =  5.0
>
> Unless you've compiled with double precision, it is unlikely you will
> achieve a
> minimal force this low.  The use of restraints is going to preclude most
> movement in the system, so don't be surprised if grompp does not (and
> cannot)
> achieve this tolerance.
>
>> emstep  =  0.01
>> implicit_solvent=  GBSA
>> gb_algorithm=   HCT
>> nstgbradii  =  1
>> rgbradii=  1
>
> This should also be set to zero if the above neighbor searching parameters
> are zero.
>
>> gb_epsilon_solvent  =  80
>> gb_saltconc   =  0
>> sa_algorithm=  Ace-approximation
>> sa_surface_tension  = -1
>>
>> Additionally I have a question according to the vdwtype and coulombtype.
>> Why do I have to set the two parameters to cutoff?
>>
>
> Because settings like PME don't make sense for implicit solvent
> calculations.
> Plain cutoffs with finite values are almost never adequate for any
> purpose, however.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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.
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Re: [gmx-users] Errors in Minimization using grompp




On 6/13/12 7:55 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi!
Thank you for your answer.


On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.


Doesn't really matter - nothing will move more than a fraction of an
Angstrom unless it's horribly wrong, in which case not moving the heavy
atoms won't help you.


   And I want to do this with implicit solvent.


Probably not worth the effort if you're just preparing for MD.


Our goal is not an MD simulation of the protein. We plan a
Poisson-Boltzmann electrostatics calculation. For that we need the heavy
atoms as they are in the crystal structure (even 1 Angstroem movement
would be too much) with good hydrogen atom position.


With restraints on heavy atoms, your positions will not deviate very much at 
all.  A 1 Angstrom movement would be huge in this case; I would expect your 
deviations to be orders of magnitude less.



We need to minimize, simulate, minimize, simulate the hydrogen atoms.


I don't follow the logic here.  You say you need to do an EM of the H atoms in 
order to do some PBSA calculation with no MD, but here you're doing two 
iterations of EM and MD.



Implicit solvent is ok for us. (For a later MD run of the complete
protein, we will use explicit solvent).

This is the .mdp file:



There are several problems here, most of which I've already stated, but I'll 
recapitulate them again.




define  =  -DPOSRES
constraints =  all-bonds
integrator  =  steep
nsteps  =  3
vdwtype =  cutoff
coulombtype =  cutoff


As Mark said, these settings should be "cut-off" not "cutoff."


epsilon_rf = 0
pbc =  xyz


For an implicit system, periodicity should be set to "no" and grompp will warn 
you about using angular COM removal (invoked below) if you leave it set as is.



nstlist =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.2
rvdw=  1.2


Finite cutoffs with implicit solvent will lead to instability and poor energy 
conservation.  These three lines (rlist, rcoulomb, rvdw) should be set to zero, 
unless you're satisfied with artifacts.



rvdw_switch = 0.7


This setting has no effect when using cutoffs.


comm-mode   =  angular
comm-grps   =  System
nstcgsteep = 1000
emtol   =  5.0


Unless you've compiled with double precision, it is unlikely you will achieve a 
minimal force this low.  The use of restraints is going to preclude most 
movement in the system, so don't be surprised if grompp does not (and cannot) 
achieve this tolerance.



emstep  =  0.01
implicit_solvent=  GBSA
gb_algorithm=   HCT
nstgbradii  =  1
rgbradii=  1


This should also be set to zero if the above neighbor searching parameters are 
zero.


gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm=  Ace-approximation
sa_surface_tension  = -1

Additionally I have a question according to the vdwtype and coulombtype.
Why do I have to set the two parameters to cutoff?



Because settings like PME don't make sense for implicit solvent calculations. 
Plain cutoffs with finite values are almost never adequate for any purpose, however.


-Justin

--


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




--
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Re: [gmx-users] Errors in Minimization using grompp

Hi!
Thank you for your answer.

> On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want to do a minimization of the hydrogens of my protein. Only the
>> hydrogens.
>
> Doesn't really matter - nothing will move more than a fraction of an
> Angstrom unless it's horribly wrong, in which case not moving the heavy
> atoms won't help you.
>
>>   And I want to do this with implicit solvent.
>
> Probably not worth the effort if you're just preparing for MD.

Our goal is not an MD simulation of the protein. We plan a
Poisson-Boltzmann electrostatics calculation. For that we need the heavy
atoms as they are in the crystal structure (even 1 Angstroem movement
would be too much) with good hydrogen atom position.
We need to minimize, simulate, minimize, simulate the hydrogen atoms.
Implicit solvent is ok for us. (For a later MD run of the complete
protein, we will use explicit solvent).

This is the .mdp file:


define  =  -DPOSRES
constraints =  all-bonds
integrator  =  steep
nsteps  =  3
vdwtype =  cutoff
coulombtype =  cutoff
epsilon_rf = 0
pbc =  xyz
nstlist =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.2
rvdw=  1.2
rvdw_switch = 0.7
comm-mode   =  angular
comm-grps   =  System
nstcgsteep = 1000
emtol   =  5.0
emstep  =  0.01
implicit_solvent=  GBSA
gb_algorithm=   HCT
nstgbradii  =  1
rgbradii=  1
gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm=  Ace-approximation
sa_surface_tension  = -1

Additionally I have a question according to the vdwtype and coulombtype.
Why do I have to set the two parameters to cutoff?

Eva


>
>> All the time when I try it there are errors in my .mdp file. Can you
>> please give me an example how such a .mdp file should look like.
>
> Every tutorial you've done will have an example EM .mdp file. Searching
> Google for some implicit solvent examples will provide some leads.
> Ultimately you need to learn how to create and manage one, so hoping one
> will appear and using it blindly is not terribly productive.
>



> Mark
> --
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Re: [gmx-users] unknown residue (BGC)




On 6/13/12 7:48 AM, delara aghaie wrote:

Dear Justin
Thanks again for your response.
About renaming residue would you pls explain more? On which basis I should
select the new name?



The contents of the .pdb file and/or the RCSB website from which you downloaded 
the file will tell you the exact chemical identity of the unknown species.  Once 
you have identified what it is, you can choose a suitable name from the known 
residues in the force field.



Also about repairing the pdb file, can you pls introduce me a free suitable
program for this if exists?



Spend a few minutes Googling.  You will find numerous potential solutions.

-Justin

--


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




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Re: [gmx-users] input/output error in production grompp




On 6/13/12 7:36 AM, Malai wrote:

Hi,

I used the command following to generate .tpr file for production but I got the
following error. Without considering this error, I run production but it is
working now. any problem will be in production?



The command below makes no sense; how is it that you were able to produce a .tpr 
file for your simulation?



-v -f hex1.mpb -c hex1.pdb -p hex1.top -o hex1.pdb



This is not the command you typed (it contains several errors, both logical and 
typographical), and it certainly has nothing to do with the error below, as no 
reference is made to a file called "hex1.gro."  When reporting problems, please 
always copy and paste directly from your terminal.  Re-typing what you think you 
typed is error prone and wastes time.



Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491

File input/output error:
hex1.gro
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



I/O errors occur when either a file isn't found in the working directory (i.e. 
doesn't exist) or can't be produced (insufficient permission or disk space to 
write the file).


-Justin

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] input/output error in production grompp

Hi,

I used the command following to generate .tpr file for production but I got
the following error. Without considering this error, I run production but
it is working now. any problem will be in production?

-v -f hex1.mpb -c hex1.pdb -p hex1.top -o hex1.pdb

Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491

File input/output error:
hex1.gro
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Many Thanks.

Malai
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Re: [gmx-users] unknown residue (BGC)

On 6/13/12 6:32 AM, delara aghaie wrote:

Dear Gromacs users
I want to create from 1AU1.pdb, the .gro and .top files.

Running this command

pdb2gmx -ignh -f 1AU1.pdb -o 1AU1.gro -p topo.top -water spce

and choose this forcefield:

GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

I get this error:
Fatal error:
Residue 'BGC' not found in residue topology database
How can i fix it?

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

In this case, simply renaming the residue is probably all that is necessary.
53A6 has parameters for sugars.

Also what this message by pdb2gmx means?
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

There are missing residues in the PDB structure. The header of the file tells
you which ones are missing. You will need to reconstruct their positions with
some external modeling software before proceeding.

-Justin

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

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[gmx-users] unknown residue (BGC)

2012-06-13 Thread delara aghaie

Dear Gromacs users
I want to create from 1AU1.pdb, the  .gro and .top files.

Running this command

pdb2gmx -ignh -f 1AU1.pdb -o 1AU1.gro -p topo.top -water spce

and choose this forcefield: 


 GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

I get this error:
Fatal error:
Residue 'BGC' not found in residue topology database

How can i fix it?

Also what this message by pdb2gmx means?
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully


Thanks
Regards
D.M
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Re: [gmx-users] Re: Positive Potential Energy after equilibration




On 6/13/12 4:29 AM, Satish Kamath wrote:

Dear Sir,

I removed the H-H 1-4 interaction from pairs and this seems to have lowered
the potential a lot to 10^2 from 9000 but is still positive. But is it a
valid thing to do?



Haphazardly deleting energetic terms to produce a more desirable energy is a 
poor strategy for parameterization.


-Justin

--


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




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Re: [gmx-users] question about pdb file

2012-06-13 Thread Mike M

>
> Dear Gromacs users
> I have encountered in pdb data bank with Human interferon crystal
> structure:
> PDB ID : 1ITF
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF
>
>  It is mentioned that it contains 24 structures. I opened the file and
> saw there are 24 models there.
>
>  Now if I want to do some simulations on this protein, how should I know
> which model to select
>
>
> You get 24 model because that structure was not determined by X-Ray
> diffraction, but by NMR. With the structure calculation from the X-Ray data
> you obtain a single converged structure, whereas by NMR you get an ensemble
> of all conformations that have been detected in your sample solution.
>

   You can use any of the 24 structures, since you are going to perform a
MD run. During your running, the other 23 conformations are likely to be
visited.

>
>   and when doing pdb2gmx, I should delete the other models?
>
> Yup, just use one model.
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Re: [gmx-users] (no subject)




On 6/13/12 5:09 AM, Seera Suryanarayana wrote:

Dear all gromacs users,

  I am doing moleculer dynamics by using gromacs software.I
got the following error after using the commond" mdrun -deffnm nvt".

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated.

Kindly tell me how to overcome this error.



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

-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] (no subject)

2012-06-13 Thread Seera Suryanarayana

Dear all gromacs users,

 I am doing moleculer dynamics by using gromacs
software.I got the following error after using the commond" mdrun -deffnm
nvt".

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated.

Kindly tell me how to overcome this error.

Suryanarayana Seera,
JRF,
India.
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Re: [gmx-users] Errors in Minimization using grompp


On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.


Doesn't really matter - nothing will move more than a fraction of an 
Angstrom unless it's horribly wrong, in which case not moving the heavy 
atoms won't help you.



  And I want to do this with implicit solvent.


Probably not worth the effort if you're just preparing for MD.


All the time when I try it there are errors in my .mdp file. Can you
please give me an example how such a .mdp file should look like.


Every tutorial you've done will have an example EM .mdp file. Searching 
Google for some implicit solvent examples will provide some leads. 
Ultimately you need to learn how to create and manage one, so hoping one 
will appear and using it blindly is not terribly productive.


Mark
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[gmx-users] Errors in Minimization using grompp

Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens. And I want to do this with implicit solvent.
All the time when I try it there are errors in my .mdp file. Can you
please give me an example how such a .mdp file should look like.

Thank you,
Eva

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Re: [gmx-users] error in grompp run

> On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi,
>> I want to do a MD simulation in vacuum.
>
> So don't turn on implicit solvent.
Sorry,
my fault. I want to do it in implicit solvent.
>
>>   So first I wanted to prepare the
>> files for that with "grompp".
>> But there I got the error that
>> "With GBSA implicit solvent, rgbradii must be equal to rlist"
>>
>> But the 2 values are the same in my .mdp file. Can you please show me
>> where the failure is?
>>
>>
>> define  = -DPOSRES
>> integrator  =  md
>> emtol = 1000.0
>> emstep = 0.01
>> nsteps  =  5
>> nstlist =  1
>> ns_type =  simple
>> rgbradii= 0
>> rlist   =  0
>> coulombtype =  cutoff
>> vdwtype =  cutoff
>
> These are misspelled.
>
> See manual 7.3.9 for how to simulate without cut-offs.
>
> Mark
>
>> rcoulomb=  0
>> rvdw=  0
>> pbc =  no
>> epsilon_rf  =  0
>>
>> implicit_solvent= GBSA
>> gb_algorithm= HCT
>> gb_epsilon_solvent  = 78.3
>>
>> nstxout = 1
>> nstfout = 1
>> nstvout = 1
>> nstxtcout   = 1
>> nstlog  = 1
>>
>>
>>
>> Thank you,
>> Eva
>>
>
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[gmx-users] Re: Positive Potential Energy after equilibration

2012-06-13 Thread Satish Kamath

Dear Sir,

I removed the H-H 1-4 interaction from pairs and this seems to have lowered
the potential a lot to 10^2 from 9000 but is still positive. But is it a
valid thing to do?


Satish Kamath
IISc Bangalore
India

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Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] error in grompp run


On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi,
I want to do a MD simulation in vacuum.


So don't turn on implicit solvent.


  So first I wanted to prepare the
files for that with "grompp".
But there I got the error that
"With GBSA implicit solvent, rgbradii must be equal to rlist"

But the 2 values are the same in my .mdp file. Can you please show me
where the failure is?


define  = -DPOSRES
integrator  =  md
emtol = 1000.0
emstep = 0.01
nsteps  =  5
nstlist =  1
ns_type =  simple
rgbradii= 0
rlist   =  0
coulombtype =  cutoff
vdwtype =  cutoff


These are misspelled.

See manual 7.3.9 for how to simulate without cut-offs.

Mark


rcoulomb=  0
rvdw=  0
pbc =  no
epsilon_rf  =  0

implicit_solvent= GBSA
gb_algorithm= HCT
gb_epsilon_solvent  = 78.3

nstxout = 1
nstfout = 1
nstvout = 1
nstxtcout   = 1
nstlog  = 1



Thank you,
Eva



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[gmx-users] error in grompp run