[gmx-users] Viscosity Calculation in Gromacs V5.1.5

[Sabreen Farnaz]

Dear all,

I am applying an electric field to water and I need to calculate its
viscosity at different simulation temperature. I have come across gmx
energy -vis option that outputs shear and bulk viscosity. And another way
is to use gmx tcaf -ov and then apply correction. Since I do not have an
acceleration group, which one will give the correct answer? What is the
difference between the shear viscosities by the two commands?
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Re: [gmx-users] Pressure Calculation in Gromacs

[Brandon Wiebe]

Thank you, Justin.

So if I wanted to simulate a system of Lennard-Jones particles under the NPT 
ensemble using reduced units, would I need to set ref_p to P*, or PRESFAC*(P*)?

Regards,
Brandon

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Monday, July 16, 2018 7:23 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure Calculation in Gromacs

On 7/16/18 9:55 PM, Brandon Wiebe wrote:
> Hi there,
>
> I am wondering if anyone can break down exactly how the instantaneous 
> pressure of any given frame is calculated in Gromacs?
>
> According to section 3.4.3 of the manual, the pressure tensor is given by: P 
> = (2/V) * (Ek - W), where Ek is kinetic energy and W is the virial.
> I have taken a particular frame and calculated the volume, kinetic energy and 
> virial.
> My calculated quantities all match quite closely with the values reported by 
> Gromacs, however, the pressure that I get is significantly lower than the 
> value reported by Gromacs.
> The elements of my calculated pressure tensor are all approximately 16.5 
> times smaller than those reported by Gromacs, even though the component 
> quantities that go into the pressure calculation are nearly identical.

There's a unit conversion factor (see src/gromacs/math/units.h):

/* Pressure in MD units is:
  * 1 bar = 1e5 Pa = 1e5 kg m^-1 s^-2 = 1e-28 kg nm^-1 ps^-2 = 1e-28 /
AMU amu nm^1 ps ^2
  */
#define BAR_MDUNITS  (1e5*NANO*PICO*PICO/AMU)
#define PRESFAC  (1.0/BAR_MDUNITS)

PRESFAC works out to be 16.6.

-Justin

> I have repeated this calculation for a number of frames, and have tried using 
> Gromacs 4.6.7 and 5.0.4 to no avail.
> Clearly there is some systematic error in my methodology, where could this 
> discrepancy come from?
>
> Regards,
> Brandon

--
==

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

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

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

==

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Re: [gmx-users] Pressure Calculation in Gromacs

[Justin Lemkul]

On 7/16/18 9:55 PM, Brandon Wiebe wrote:

Hi there,

I am wondering if anyone can break down exactly how the instantaneous pressure 
of any given frame is calculated in Gromacs?

According to section 3.4.3 of the manual, the pressure tensor is given by: P = 
(2/V) * (Ek - W), where Ek is kinetic energy and W is the virial.
I have taken a particular frame and calculated the volume, kinetic energy and 
virial.
My calculated quantities all match quite closely with the values reported by 
Gromacs, however, the pressure that I get is significantly lower than the value 
reported by Gromacs.
The elements of my calculated pressure tensor are all approximately 16.5 times 
smaller than those reported by Gromacs, even though the component quantities 
that go into the pressure calculation are nearly identical.


There's a unit conversion factor (see src/gromacs/math/units.h):

/* Pressure in MD units is:
 * 1 bar = 1e5 Pa = 1e5 kg m^-1 s^-2 = 1e-28 kg nm^-1 ps^-2 = 1e-28 / 
AMU amu nm^1 ps ^2

 */
#define BAR_MDUNITS  (1e5*NANO*PICO*PICO/AMU)
#define PRESFAC  (1.0/BAR_MDUNITS)

PRESFAC works out to be 16.6.

-Justin


I have repeated this calculation for a number of frames, and have tried using 
Gromacs 4.6.7 and 5.0.4 to no avail.
Clearly there is some systematic error in my methodology, where could this 
discrepancy come from?

Regards,
Brandon


--
==

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

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

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

==

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[gmx-users] Pressure Calculation in Gromacs

[Brandon Wiebe]

Hi there,

I am wondering if anyone can break down exactly how the instantaneous pressure 
of any given frame is calculated in Gromacs?

According to section 3.4.3 of the manual, the pressure tensor is given by: P = 
(2/V) * (Ek - W), where Ek is kinetic energy and W is the virial.
I have taken a particular frame and calculated the volume, kinetic energy and 
virial.
My calculated quantities all match quite closely with the values reported by 
Gromacs, however, the pressure that I get is significantly lower than the value 
reported by Gromacs.
The elements of my calculated pressure tensor are all approximately 16.5 times 
smaller than those reported by Gromacs, even though the component quantities 
that go into the pressure calculation are nearly identical.

I have repeated this calculation for a number of frames, and have tried using 
Gromacs 4.6.7 and 5.0.4 to no avail.
Clearly there is some systematic error in my methodology, where could this 
discrepancy come from?

Regards,
Brandon
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[gmx-users] Incorrect number of parameters in improper dihedral

[Debadutta Prusty]

Hi everyone,

I ran an energy minimization run on a single polymer chain. On running the
gmx grompp  -f  .mdp , I get the following error message:
"ERROR 1 [file topol.top, line 1486]:
 Incorrect number of parameters - found 3, expected 2 or 4 for Improper
 Dih."

The corresponding line(line 1486) in the topology file is:
;  aiajakal functc0c1
c2c3
8 7 115 2improper_X_CA_Y_Z

The entry containing the definition of this forcefield in the ffbonded.itp
(I am using opls all atom force field) file is
; X-CA-Y-Z improper torsion. CA is any ring carbon in pyridine
#define improper_X_CA_Y_Z   180.0 10.460 2

The topology file for the above polymer was generated by using the command
pdb2gmx(it operated on the pdb file of the polymer chain).

Please help me out.
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Re: [gmx-users] x2top_error

[Alex]

x2top is finding atoms with more nearest neighbors than what you have in
your ff. Make sure the box that contains your CNT is of appropriate size,
especially along the CNT axis.

Alex

On Mon, Jul 16, 2018 at 3:10 PM, Atila Petrosian 
wrote:

>  Hi gromacs users,
>
> I used following command for CNT.
>
> gmx_mpi x2top –f cnt.gro –o cnt.top –ff cnt –name CNT –pbc -noparam
>
>
> I encountered with:
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> Can not find forcefield for atom CA-968 with 5 bonds
>
> Can not find forcefield for atom CA-970 with 5 bonds
>
> Can not find forcefield for atom CA-971 with 1 bonds
>
> Can not find forcefield for atom CA-972 with 5 bonds
>
> Can not find forcefield for atom CA-974 with 5 bonds
>
> Can not find forcefield for atom CA-975 with 1 bonds
>
> Can not find forcefield for atom CA-976 with 5 bonds
>
> Can not find forcefield for atom CA-978 with 5 bonds
>
> Can not find forcefield for atom CA-979 with 1 bonds
>
> Can not find forcefield for atom CA-980 with 5 bonds
>
> Can not find forcefield for atom CA-982 with 5 bonds
>
> Can not find forcefield for atom CA-983 with 1 bonds
>
> Can not find forcefield for atom CA-984 with 5 bonds
>
> Can not find forcefield for atom CA-986 with 5 bonds
>
> Can not find forcefield for atom CA-987 with 1 bonds
>
> Can not find forcefield for atom CA-988 with 5 bonds
>
> Can not find forcefield for atom CA-990 with 5 bonds
>
> Can not find forcefield for atom CA-991 with 1 bonds
>
> Can not find forcefield for atom CA-992 with 5 bonds
>
> Can not find forcefield for atom CA-994 with 5 bonds
>
> Can not find forcefield for atom CA-995 with 1 bonds
>
> Can not find forcefield for atom CA-996 with 5 bonds
>
> Can not find forcefield for atom CA-998 with 5 bonds
>
> Can not find forcefield for atom CA-999 with 1 bonds
>
> Can not find forcefield for atom CA-1000 with 5 bonds
>
> Can not find forcefield for atom CA-1002 with 5 bonds
>
> Can not find forcefield for atom CA-1003 with 1 bonds
>
> Can not find forcefield for atom CA-1004 with 5 bonds
>
> Can not find forcefield for atom CA-1006 with 5 bonds
>
> Can not find forcefield for atom CA-1007 with 1 bonds
>
> Can not find forcefield for atom CA-1008 with 5 bonds
>
>
>
> I have a directory (cnt.ff) in current directory and the content of n2t
> file is as follows:
>
> CCA0.0012.011  3C 0.141   C 0.141   C 0.141
> CCA0.0012.011  2C 0.141   C 0.141
>
> How to resolve this error?
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[gmx-users] x2top_error

[Atila Petrosian]

 Hi gromacs users,

I used following command for CNT.

gmx_mpi x2top –f cnt.gro –o cnt.top –ff cnt –name CNT –pbc -noparam


I encountered with:

.

.

.

.

.

.

Can not find forcefield for atom CA-968 with 5 bonds

Can not find forcefield for atom CA-970 with 5 bonds

Can not find forcefield for atom CA-971 with 1 bonds

Can not find forcefield for atom CA-972 with 5 bonds

Can not find forcefield for atom CA-974 with 5 bonds

Can not find forcefield for atom CA-975 with 1 bonds

Can not find forcefield for atom CA-976 with 5 bonds

Can not find forcefield for atom CA-978 with 5 bonds

Can not find forcefield for atom CA-979 with 1 bonds

Can not find forcefield for atom CA-980 with 5 bonds

Can not find forcefield for atom CA-982 with 5 bonds

Can not find forcefield for atom CA-983 with 1 bonds

Can not find forcefield for atom CA-984 with 5 bonds

Can not find forcefield for atom CA-986 with 5 bonds

Can not find forcefield for atom CA-987 with 1 bonds

Can not find forcefield for atom CA-988 with 5 bonds

Can not find forcefield for atom CA-990 with 5 bonds

Can not find forcefield for atom CA-991 with 1 bonds

Can not find forcefield for atom CA-992 with 5 bonds

Can not find forcefield for atom CA-994 with 5 bonds

Can not find forcefield for atom CA-995 with 1 bonds

Can not find forcefield for atom CA-996 with 5 bonds

Can not find forcefield for atom CA-998 with 5 bonds

Can not find forcefield for atom CA-999 with 1 bonds

Can not find forcefield for atom CA-1000 with 5 bonds

Can not find forcefield for atom CA-1002 with 5 bonds

Can not find forcefield for atom CA-1003 with 1 bonds

Can not find forcefield for atom CA-1004 with 5 bonds

Can not find forcefield for atom CA-1006 with 5 bonds

Can not find forcefield for atom CA-1007 with 1 bonds

Can not find forcefield for atom CA-1008 with 5 bonds



I have a directory (cnt.ff) in current directory and the content of n2t
file is as follows:

CCA0.0012.011  3C 0.141   C 0.141   C 0.141
CCA0.0012.011  2C 0.141   C 0.141

How to resolve this error?
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Re: [gmx-users] Problems during installation

[Justin Lemkul]

On 7/16/18 1:42 PM, Rajat Desikan wrote:

Hi Mark,

Thank you for the quick answer. My group is experimenting with a GPU-heavy
processor-light configuration similar to the Amber machines available from
Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
understanding, for this configuration to be successful performance-wise,
gromacs would've to do all the calculating on GPUs, and not just
electrostatics. That's why we're looking at openmm enabled versions.

If you and others have alternate suggestions, we would be really eager to
hear them. Thank you for your time.


IIRC, the OpenMM code in GROMACS only ever did implicit solvent 
calculations. With GROMACS 2018, all the nonbonded calculations are done 
on GPU with PME offload, which sounds exactly like what you want. You 
should be using a current version, not an ancient one :)


-Justin


Regards,
Rajat

On Mon, 16 Jul 2018, 10:25 pm Mark Abraham, 
wrote:


Hi,

This code was not ever functional in the 4.6 branch, so if you want it to
work, try 4.5.7. But really there is no reason to want to build it any more
- use the CUDA and OpenCL ports available in more recent GROMACS.

Mark

On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan 
wrote:


Dear all,
I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
strange error while running make:

/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function

‘cmain’:

/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
missing braces around initializer [-Wmissing-braces]
gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
^
*/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
initialization for ‘hw_opt’)*
*/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’; did
you mean ‘gpu_opt’?*
* { "-gpu_id",  FALSE, etSTR, {_opt.gpu_id},*
  ^
src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
make[2]: ***

[src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]

Error 1
CMakeFiles/Makefile2:1902: recipe for target
'src/kernel/CMakeFiles/mdrun.dir/all' failed
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2

I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
software, so I'm at a loss. Please help me out. Google did not have much
leads.

Thank you.

Regards,
Rajat

--
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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--
==

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

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

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

==

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Re: [gmx-users] Problems during installation

[Rajat Desikan]

Hi Mark,

Thank you for the quick answer. My group is experimenting with a GPU-heavy
processor-light configuration similar to the Amber machines available from
Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
understanding, for this configuration to be successful performance-wise,
gromacs would've to do all the calculating on GPUs, and not just
electrostatics. That's why we're looking at openmm enabled versions.

If you and others have alternate suggestions, we would be really eager to
hear them. Thank you for your time.

Regards,
Rajat

On Mon, 16 Jul 2018, 10:25 pm Mark Abraham, 
wrote:

> Hi,
>
> This code was not ever functional in the 4.6 branch, so if you want it to
> work, try 4.5.7. But really there is no reason to want to build it any more
> - use the CUDA and OpenCL ports available in more recent GROMACS.
>
> Mark
>
> On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan 
> wrote:
>
> > Dear all,
> > I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
> > i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> > strange error while running make:
> >
> > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
> ‘cmain’:
> > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> > missing braces around initializer [-Wmissing-braces]
> >gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
> >^
> > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
> > initialization for ‘hw_opt’)*
> > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> > ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’; did
> > you mean ‘gpu_opt’?*
> > * { "-gpu_id",  FALSE, etSTR, {_opt.gpu_id},*
> >  ^
> > src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> > 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> > make[2]: ***
> [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> > Error 1
> > CMakeFiles/Makefile2:1902: recipe for target
> > 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> > make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
> > software, so I'm at a loss. Please help me out. Google did not have much
> > leads.
> >
> > Thank you.
> >
> > Regards,
> > Rajat
> >
> > --
> > Dr. Rajat Desikan (Post Doctoral Fellow)
> > Prof. Narendra M Dixit's Lab (no 1),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Negative pressure in NVT simulation

[Diana Lousa]

Hello,

Following this subject, if one wants to do a simulation with freeze groups
using the Verlet cutoff scheme in order to make efficient use of GPU
processing is it possible to use energy group exclusions? I tried it a
while ago (I am not sure if it was version 5.1 or 2016) and received an
error message saying that energy_grp_exclusions could not be used with the
Verlet schemce. If this is not possible how should one proceed to perform
simulations with freeze groups with the Verlet scheme?

Thanks in advance,

Best regards

Diana

On Sun, Jul 15, 2018 at 7:39 PM, Justin Lemkul  wrote:

>
>
> On 7/15/18 2:32 PM, Neda Rafiee wrote:
>
>> ;
>> energygrps  = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil
>> OGem OMB SIB SiSil SiGem HSil HGem OW HW
>> energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW
>> SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW
>> OGem OXB OW
>>
>> freezegrps  = SIB OXB OMB SiSil OSil SiGem OGem
>> freezedim   = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
>>
>
> You're not using energy group exclusions, which the manual recommends when
> freezing:
>
> "To avoid spurious contributions to the virial and pressure due to large
> forces between completely frozen atoms you need to use energy group
> exclusions, this also saves computing time."
>
> http://manual.gromacs.org/documentation/current/user-guide/
> mdp-options.html#non-equilibrium-md
>
> Freezing is a very severe artificial perturbation, so you will have to use
> hacks like that if you intend to do a simulation with so many things frozen.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Diana Lousa
Post-doc
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
-- 
Gromacs Users mailing list

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Re: [gmx-users] Problems during installation

[Mark Abraham]

Hi,

This code was not ever functional in the 4.6 branch, so if you want it to
work, try 4.5.7. But really there is no reason to want to build it any more
- use the CUDA and OpenCL ports available in more recent GROMACS.

Mark

On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan 
wrote:

> Dear all,
> I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
> i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> strange error while running make:
>
> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function ‘cmain’:
> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> missing braces around initializer [-Wmissing-braces]
>gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
>^
> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
> initialization for ‘hw_opt’)*
> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’; did
> you mean ‘gpu_opt’?*
> * { "-gpu_id",  FALSE, etSTR, {_opt.gpu_id},*
>  ^
> src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> Error 1
> CMakeFiles/Makefile2:1902: recipe for target
> 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
>
> I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
> software, so I'm at a loss. Please help me out. Google did not have much
> leads.
>
> Thank you.
>
> Regards,
> Rajat
>
> --
> Dr. Rajat Desikan (Post Doctoral Fellow)
> Prof. Narendra M Dixit's Lab (no 1),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
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[gmx-users] Problems during installation

[Rajat Desikan]

Dear all,
I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
strange error while running make:

/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function ‘cmain’:
/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
missing braces around initializer [-Wmissing-braces]
   gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
   ^
*/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
initialization for ‘hw_opt’)*
*/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’; did
you mean ‘gpu_opt’?*
* { "-gpu_id",  FALSE, etSTR, {_opt.gpu_id},*
 ^
src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
Error 1
CMakeFiles/Makefile2:1902: recipe for target
'src/kernel/CMakeFiles/mdrun.dir/all' failed
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2

I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
software, so I'm at a loss. Please help me out. Google did not have much
leads.

Thank you.

Regards,
Rajat

-- 
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- 
Gromacs Users mailing list

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Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

[Mark Abraham]

Hi,

No idea sorry. I never attempt anything like this, in part because frozen
groups are anyway unphysical.

Mark

On Mon, Jul 16, 2018 at 2:56 PM Neda Rafiee  wrote:

> Dear Mark,
> I removed different residues from my energy group list, but still the
> problem of very large negative pressure exist. Any other solution?
> Thanks in advance.
> Neda
>
>
> - Original Message -
> From: Neda Rafiee 
> To: gmx-us...@gromacs.org
> Sent: Mon, 16 Jul 2018 12:03:34 +0430 (IRDT)
> Subject: Re: [gmx-users][Spam-FG]
>  [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
> Dear Mark,
> Thanks a lot for your useful suggestions
> Neda
>
>
> - Original Message -
> From: Mark Abraham 
> To: gmx-us...@gromacs.org
> Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT)
> Subject: Re: [gmx-users] [Spam-FG]
> [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
> Hi,
>
> I presume that's because you still have interactions between groups that
> are frozen.
>
> You can make your life easier by using only the groups you need for your
> simulation, e.g. those needing a table and those that are frozen. If you
> are trying to get per-residue decomposition, then (first) make sure your
> force field was parametrized such that this is meaningful (most aren't),
> and prefer to do that analysis using mdrun -rerun. mdrun goes slower for
> each energy group that has interactions to compute, so minimize that.
>
> I would also have done a simulation with just my slab and found this
> pressure issue back then. It is good practice to add complexity to models
> incrementally, after validating your expectations on the simulation at the
> previous stage.
>
> Mark
>
> On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee  wrote:
>
> > Dear Justin,
> > I added the following energy exclusion pairs to my mdp file. Now
> potential
> > energy decreased significantly but still I have a very large negative
> > pressure (minus 10 to power 28) in my system. It seems that pressure is
> the
> > same as before.Should I do anything else?
> >
> > energygrp-excl= SIB SIB  SIB OXB  SIB OMB  SIB SiSil  SIB OSil  SIB SiGem
> > SIB OGem  OXB OXB  OXB OMB  OXB SiSil  OXB OSil  OXB SiGem  OXB OGem  OMB
> > OMB  OMB SiSil  OMB OSil  OMB SiGem  OMB OGem  SiSil SiSil  SiSil OSil
> > SiSil SiGem  SiSil OGem  OSil OSil  OSil SiGem  OSil OGem  SiGem SiGem
> > SiGem OGem  OGem OGem
> >
> > Thanks
> > Neda
> >
> > - Original Message -
> > From: Neda Rafiee 
> > To: gmx-us...@gromacs.org
> > Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
> > Subject: [Spam-FG][gmx-users]
> > [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
> >
> > http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1
> >
> >
> VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBF
> >
> >
> AfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI
> > <
> http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBFAfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI
> >
> >
> >
> LWEQ2RCwUXkgZeEkyBUJYOgZGVh1NNndURHxnOl9iWiYOZjQVNj12HEN1WDUrZgA6LUEiFhM1BlQ
> >
> >
> He2QiEEZpC2cvDSIBDH5kEXRRJgNuVycBbD05ESluekcIaiwDZmUNKWgdExQXWHYudwYRLHFAJAF
> >
> >
> zLTM*MXlkEXh1IgB2YCooczcpFRBSehFzexctcjxmJWdVBisxU0csZmI5LnF3KTBkMxU6MHVYP2J
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> >
> EdGgjM2xqJWVxeXg7RhddVhkDVl0sHFFLFB0NNCx2MzN0aCMxbGowAhwBVUFfE0NANA9RXgELRhZ
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> >
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> >
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> >
> >
> RYkAVAl9AJmBJXidxKAA4PlBqPndyPztLRjUsTiM*PhANeTRWVzs9Ygk2KVIKNTEUUCF8YGIMPmZ
> >
> pBC9iM0A4IXUcGX1rHAdtYwBecT1BHRp8ejRkex8MYHQuDUEtIw06cUczVHQMAHtmLSdgMxoKIn
> >
> >
> B.IGh3DABGaToBazAaKHU.ajRaRDwpW3AiPXQgEy8sehwXcnYMCmReADB9ZXF5ejQsdjEzdGh9WR
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> >
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> >
> lcVwRFTEEYA0oLAlcQQEEaEl0bBg5UHR9MCRgbCl1ZGxxeEGgjMW5qJWVweXg0Nx5FRwRSDB4bHV
> >
> >
> JLBREdWEkbWkYYBEJTQglKCHF5eDYsdjEzdGgjCgQeURVLVldDWwEfVAYHTlAPGQsKAx5XZ1kGQV
> >
> >
> wGHAx8DQNJDB8eJ3hFBUVAWy9uaUE*VgADCid4RQVFM3RoITFsaiVlcXlUXFgCQQlbR1RGG0RCFx
> >
> >
> 4UGVdfWF5BE0dwRBwaShcFVjVVRRpYXRM3b1gfHlZlcXl6NCx2MTN0aGFZGB5VFktWV1lNH11fHR
> >
> >
> tXHx8TVksaDRAaXxMeXhUBT1wNBAoJGAoMXUIQXhwTGkxcDQlWSx4LH2tLG0keARtGQx9qJWVzeX
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> >
> g0LHYxM2kPTklBH1YAAwpVRkkHRFYHHGNWHgVIBBIKVlteETEzdGwjMWxqJWVxYXg0LHcxM3v0yu
> > ILmFi9OA8Sb.IVubYVMyMxbG4lZXF5eDQsbjEzdGojMW0HyGY2m9p1eztByEYRoCDQ3g__"
> > target="_blank">
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> >
> >
> hSxtJHgEbRkMfKkIXHhQZV19YXkETaCMxbmolZXF5eDRqHkVHBFIMHgIFVhUQFBVRXlhfVgBHcEQ
> > <
> 

Re: [gmx-users] gromacs 2018 compilation problem with stdlib

[Mark Abraham]

Hi,

Unfortunately the list cannot accept attachments.

Those examples intend for you to replace "/path/to/gcc" with the path to
your gcc, e.g. /usr/local/bin/gcc-5 or whatever it is. Thus for example

-DGMX_STDLIB_CXX_FLAGS=-gcc-name=/usr/local/bin/gcc-5

Mark

On Mon, Jul 16, 2018 at 5:02 PM Manoel Barrionuevo 
wrote:

> Hi Mark,
>
>
> On 16/07/2018 05:09, Mark Abraham wrote:
> > Hi,
> >
> > On Sat, Jul 14, 2018 at 4:58 AM Manoel Barrionuevo 
> > wrote:
> >
> >> Hi all,
> >>
> >> I'm trying to compile gromacs 2018.2 and I would like to use intel
> >> compilers along with nvidia gpu graphic (GTX 1060) card in a desktop
> >> computer with a intel i5 quad-core cpu (the only purpose of it is for
> >> learning), in order to do so I was first following the suggested
> >> procedures at the INSTALL file distributed along with gromacs, and got
> >> the command bellow:
> >>
> >> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group
> >> /opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a
> >> /opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a
> >> /opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp
> >> -lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include"
> >> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
> >> -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DGMX_CXX_FLAGS="-g -O2
> >> -std=c++11"
> >>
> > You're doing a few things that make your life hard (or are brittle) and
> > some that make things slow. Source the appropriate script for the intel
> > compiler that you want, and then leave MKL details up to it. Choosing -O2
> > for optimization overrides the defaults for no good reason. Thus
> >
> > source /path/to/compiler/bin/compilervars.sh intel64
> > cmake ../ -DGMX_FFT_LIBRARY="mkl" -DGMX_GPU=on
> > -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
> > -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc
>
> Well, I may not get all details you pointed me however I have attached
> two files to show you what exactly happens when I do as said, first you
> will see "cmaking" file where you can find the output of cmake. I
> noticed some failures, I would be happy to hear from you what could them
> be.
>
> > It worths to say that the OS under current operation is Lubuntu (16.04)
> >> and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly
> >> without problems, however I noticed a std failure after issuing the
> >> "make" command, it says:
> >>
> >>
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250):
> >>
> >> error: namespace "std" has no member "_Exit"
> >> std:: _Exit(returnValue);
> >>   ^
> >>
> >>
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251):
> >>
> >> warning #1628: function declared with "noreturn" does retu
> >> rn
> >> }
> >> ^
> >>
> >> The same problem can be seen if I start from a very simple "cmake ../"
> >> and "make". What am I doing wrong? Is there some environment preparation
> >> step to be done prior to everything else, and what should it be?
> >>
> > On Linux, Intel compilers rely on having and finding a suitable gcc for
> the
> > standard library, so I can only presume something is messed up there. For
> > example, gcc was installed or updated after icc. Try the advice at
> >
> http://manual.gromacs.org/documentation/current/install-guide/index.html#compiler
> >
> > Mark
>
> Next, you will see in "making" attached file the output of "make".
> Again, I still seeing the issue I reported before. I haven't, however,
> set up what you suggested by looking at gromacs manual
> (
> http://manual.gromacs.org/documentation/current/install-guide/index.html#compile).
>
> I'm aware of what you just said, but I can get how should it be the
> problem since the current OS have g++-5, gcc-5, gfortran-5 and clang-5
> available, and no other gcc, g++, gfortran or clang installed and/or
> updated/available as alternative for the system.
>
> I may also point out that it would be of great help if you clarify some
> points that I got stuck since, as I said, I'm not an expert (that's why
> I got so many dumb things with my first attempt with cmake). Here they are:
>
> 1) Gromacs manual suggests this:
> |-DGMX_STDLIB_CXX_FLAGS=-gcc-name=/path/to/gcc/binary
> |
>  Where we read "-gcc-name" should I change to "-gcc-5" and give it
> the expected path. Is it?
>
> 2) Also we get this:
> |-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/path/to/gcc/lib64
> -L/path/to/gcc/lib64"
> |
>  Where we read "-rpath", should I keep it as it is or change it to
> something else? (here you can realize how much I don't know about
> compiling stuff).
>
> 3) Finally we get the last one:
> |-DCMAKE_CXX_FLAGS=--gcc-toolchain=/path/to/gcc/folder|
>
>  Where we read "-gcc-toolchain" should it be changed too? And so,
> for what?
>
> Well, I told since my very first email that the purpose of it is
> learning. I hope I will learn something from my mistakes and I do
> appreciate the kind help you 

Re: [gmx-users] gromacs 2018 compilation problem with stdlib

[Manoel Barrionuevo]

Hi Mark,


On 16/07/2018 05:09, Mark Abraham wrote:

Hi,

On Sat, Jul 14, 2018 at 4:58 AM Manoel Barrionuevo 
wrote:


Hi all,

I'm trying to compile gromacs 2018.2 and I would like to use intel
compilers along with nvidia gpu graphic (GTX 1060) card in a desktop
computer with a intel i5 quad-core cpu (the only purpose of it is for
learning), in order to do so I was first following the suggested
procedures at the INSTALL file distributed along with gromacs, and got
the command bellow:

cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group
/opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a
/opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a
/opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp
-lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include"
-DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
-DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DGMX_CXX_FLAGS="-g -O2
-std=c++11"


You're doing a few things that make your life hard (or are brittle) and
some that make things slow. Source the appropriate script for the intel
compiler that you want, and then leave MKL details up to it. Choosing -O2
for optimization overrides the defaults for no good reason. Thus

source /path/to/compiler/bin/compilervars.sh intel64
cmake ../ -DGMX_FFT_LIBRARY="mkl" -DGMX_GPU=on
-DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
-DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc


Well, I may not get all details you pointed me however I have attached 
two files to show you what exactly happens when I do as said, first you 
will see "cmaking" file where you can find the output of cmake. I 
noticed some failures, I would be happy to hear from you what could them be.



It worths to say that the OS under current operation is Lubuntu (16.04)

and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly
without problems, however I noticed a std failure after issuing the
"make" command, it says:

/home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250):

error: namespace "std" has no member "_Exit"
std:: _Exit(returnValue);
  ^

/home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251):

warning #1628: function declared with "noreturn" does retu
rn
}
^

The same problem can be seen if I start from a very simple "cmake ../"
and "make". What am I doing wrong? Is there some environment preparation
step to be done prior to everything else, and what should it be?


On Linux, Intel compilers rely on having and finding a suitable gcc for the
standard library, so I can only presume something is messed up there. For
example, gcc was installed or updated after icc. Try the advice at
http://manual.gromacs.org/documentation/current/install-guide/index.html#compiler

Mark


Next, you will see in "making" attached file the output of "make". 
Again, I still seeing the issue I reported before. I haven't, however, 
set up what you suggested by looking at gromacs manual 
(http://manual.gromacs.org/documentation/current/install-guide/index.html#compile). 
I'm aware of what you just said, but I can get how should it be the 
problem since the current OS have g++-5, gcc-5, gfortran-5 and clang-5 
available, and no other gcc, g++, gfortran or clang installed and/or 
updated/available as alternative for the system.


I may also point out that it would be of great help if you clarify some 
points that I got stuck since, as I said, I'm not an expert (that's why 
I got so many dumb things with my first attempt with cmake). Here they are:


1) Gromacs manual suggests this: 
|-DGMX_STDLIB_CXX_FLAGS=-gcc-name=/path/to/gcc/binary

|
    Where we read "-gcc-name" should I change to "-gcc-5" and give it 
the expected path. Is it?


2) Also we get this: 
|-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/path/to/gcc/lib64 -L/path/to/gcc/lib64"

|
    Where we read "-rpath", should I keep it as it is or change it to 
something else? (here you can realize how much I don't know about 
compiling stuff).


3) Finally we get the last one: 
|-DCMAKE_CXX_FLAGS=--gcc-toolchain=/path/to/gcc/folder|


    Where we read "-gcc-toolchain" should it be changed too? And so, 
for what?


Well, I told since my very first email that the purpose of it is 
learning. I hope I will learn something from my mistakes and I do 
appreciate the kind help you provided me till now.


Thanks a lot.

|
|
||

I must say that I'm not an expert on compiling things up and I got
stuck. Could someone help me out? It would be of great help to know some
tips from you guys.

Thank you all.

Kind regards,

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[  0%] Building NVCC (Device) object 

Re: [gmx-users] energy minimization

[Justin Lemkul]

On 7/16/18 3:49 AM, farial tavakoli wrote:

  Dear Justin

Thank you for your reply
I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
named topologen_1.1.pl in the working directory)
I generated my ligand topology but got this :
No output type specified. Using default type of .top
Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
Using default H type for atom 16.
Using default H type for atom 26.
Using default H type for atom 31.
Using default H type for atom 38.
Using default H type for atom 39.
Using default H type for atom 40.
Using default H type for atom 41.
Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
Using default H type for atom 47.
Using default H type for atom 48.
Using default H type for atom 49.
Using default H type for atom 50.
Using default H type for atom 51.
Using default H type for atom 52.


WARNING: Net charge on the molecule is -2.781
You will need to make corrections to the output topology


TopolGen, version 1.1_dev (10/14/2009) complete.

Output topology has been written. An attempt has been made to assign charges 
and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other
parameterization calculations have been done.  Guesses have been made for 
charge groups.  Please
inspect and correct the topology before using it in any simulations.  The 
author of the script does
NOT guarantee accuracy or usability of any of the content; TopolGen was written 
as a convenience
for outputting a skeleton topology, and nothing more.


Heed the above warning. TopolGen assigns parameters based on similarity 
to known functional groups. If your molecule has something unusual, it 
makes no attempt to try to assign reasonable parameters. You'll need to 
actually parametrize the molecule. Make use of available web servers 
like LikeParGen or others.


-Justin



the N13 atom connected to C with double bond. it sounds topolgen can not 
identify N atom in 2 bonds with C .
would you please help me to figure out this problem
thans in advanceFarial

 On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
 wrote:
  
  


On 7/15/18 1:38 AM, farial tavakoli wrote:

   Dear Justin

But I copied & pasted topolgen and perl5 folders in the working directory. and 
faced the mentioned error.

Can't open perl script "topolgen.pl": No such file or directory
I dont know how I should figure out this problem.

The problem is still the same: there's nothing called "topolgen.pl" in
the working directory. List your files, you'll see it's called something
else.


Which one of all-atom force fields will you choose to run a simulation on a 
complex with small molecule, if you want to calculate binding energy using 
G_MMPBSA ?I really need your guidance .

Presumably any of them, but I don't do such calculations.

-Justin



--
==

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

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

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

==

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Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

[Neda Rafiee]

Dear Mark,
I removed different residues from my energy group list, but still the problem 
of very large negative pressure exist. Any other solution?
Thanks in advance.
Neda


- Original Message -
From: Neda Rafiee 
To: gmx-us...@gromacs.org
Sent: Mon, 16 Jul 2018 12:03:34 +0430 (IRDT)
Subject: Re: [gmx-users][Spam-FG]   
[Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

Dear Mark,
Thanks a lot for your useful suggestions
Neda


- Original Message -
From: Mark Abraham 
To: gmx-us...@gromacs.org
Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT)
Subject: Re: [gmx-users] [Spam-FG]  
[Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

Hi,

I presume that's because you still have interactions between groups that
are frozen.

You can make your life easier by using only the groups you need for your
simulation, e.g. those needing a table and those that are frozen. If you
are trying to get per-residue decomposition, then (first) make sure your
force field was parametrized such that this is meaningful (most aren't),
and prefer to do that analysis using mdrun -rerun. mdrun goes slower for
each energy group that has interactions to compute, so minimize that.

I would also have done a simulation with just my slab and found this
pressure issue back then. It is good practice to add complexity to models
incrementally, after validating your expectations on the simulation at the
previous stage.

Mark

On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee  wrote:

> Dear Justin,
> I added the following energy exclusion pairs to my mdp file. Now potential
> energy decreased significantly but still I have a very large negative
> pressure (minus 10 to power 28) in my system. It seems that pressure is the
> same as before.Should I do anything else?
>
> energygrp-excl= SIB SIB  SIB OXB  SIB OMB  SIB SiSil  SIB OSil  SIB SiGem
> SIB OGem  OXB OXB  OXB OMB  OXB SiSil  OXB OSil  OXB SiGem  OXB OGem  OMB
> OMB  OMB SiSil  OMB OSil  OMB SiGem  OMB OGem  SiSil SiSil  SiSil OSil
> SiSil SiGem  SiSil OGem  OSil OSil  OSil SiGem  OSil OGem  SiGem SiGem
> SiGem OGem  OGem OGem
>
> Thanks
> Neda
>
> - Original Message -
> From: Neda Rafiee 
> To: gmx-us...@gromacs.org
> Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
> Subject: [Spam-FG][gmx-users]
> [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
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Re: [gmx-users] Making group of different atoms

[Chetan Puri]

*Thanks,*
*The command*
* make_ndx "a 1566 1567 1569 1571 1574 1579"  does the job of making group
of selected atoms.*

On Thu, 12 Jul 2018, 21:45 Shrinath Kumar, 
wrote:

> In the index editor of make_ndx does "a 1566 1567 1569 1571 1574 1579" not
> work? Alternatively, you can just manually make the index file as Sohaib
> suggested. An index group is just:
>
> [ name_of_group ]
> ;atomnr of atoms that make up the group eg.
> 1566 1567 1569 1571 1574 1579 etc..
>
> On 12 July 2018 at 16:24, Chetan Puri  wrote:
>
> > Yes, I have tried but I am having trouble in making a group for atoms
> with
> > different numbers.
> >
> > On Wed, 11 Jul 2018, 22:29 Quyen V. Vu,  wrote:
> >
> > > Have you try make_ndx tool of Gromacs?
> > >
> > > On Wed, Jul 11, 2018, 00:09 Chetan Puri  wrote:
> > >
> > > > Can someone guide me in how to make a group for atoms number 1566,
> > 1567,
> > > > 1569,1571,1574&1579, which all belong to a tyrosine residue number
> 128
> > of
> > > > protein.
> > > >
> > > > Since I need to measure distance between two groups (ligand and
> > protein)
> > > >
> > > >
> > > > Regards,
> > > > Chetan
> > > > --
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> or
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> > > >
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Re: [gmx-users] Help

[Mark Abraham]

Hi,

I could see that you are installing GROMACS 2018. There is the more recent
patch release called GROMACS 2018.2, which you should prefer because it
fixes some issues while doing the same job as 2018.

Mark

On Wed, Jul 11, 2018 at 2:13 PM Maximiliano Sebastián Castillo <
mcasti...@itba.edu.ar> wrote:

> Sorry, but... what is BTW 2018.2? Another software?
>
> El mié., 11 jul. 2018 a las 6:50, Mark Abraham ( >)
> escribió:
>
> > Hi,
> >
> > I haven't seen that, and don't know how to guess what might make it work.
> > BTW 2018.2 is a better idea to install.
> >
> > Mark
> >
> > On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Sebastián Castillo <
> > mcasti...@itba.edu.ar> wrote:
> >
> > > Hello,
> > > I have the next problem:
> > > [  1%] No patch step for 'fftwBuild'
> > > [  1%] No update step for 'fftwBuild'
> > > [  1%] Performing configure step for 'fftwBuild'
> > > checking for a BSD-compatible install... /usr/bin/install -c
> > > checking whether build environment is sane... configure: error: unsafe
> > > srcdir value: '/home/maximiliano/Proyecto
> > >
> Final/gromacs-2018/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild'
> > > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:109: recipe for
> > target
> > >
> >
> 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure'
> > > failed
> > > make[2]: ***
> > >
> >
> [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure]
> > > Error 1
> > > CMakeFiles/Makefile2:1440: recipe for target
> > > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> > > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > >
> > > What can I do for it?
> > > Thank you.
> > > Best regards.
> > > --
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> > > posting!
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> > >
> > --
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Re: [gmx-users] gromacs 2018 compilation problem with stdlib

[Mark Abraham]

Hi,

On Sat, Jul 14, 2018 at 4:58 AM Manoel Barrionuevo 
wrote:

> Hi all,
>
> I'm trying to compile gromacs 2018.2 and I would like to use intel
> compilers along with nvidia gpu graphic (GTX 1060) card in a desktop
> computer with a intel i5 quad-core cpu (the only purpose of it is for
> learning), in order to do so I was first following the suggested
> procedures at the INSTALL file distributed along with gromacs, and got
> the command bellow:
>
> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group
> /opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a
> /opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a
> /opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp
> -lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include"
> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
> -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DGMX_CXX_FLAGS="-g -O2
> -std=c++11"
>

You're doing a few things that make your life hard (or are brittle) and
some that make things slow. Source the appropriate script for the intel
compiler that you want, and then leave MKL details up to it. Choosing -O2
for optimization overrides the defaults for no good reason. Thus

source /path/to/compiler/bin/compilervars.sh intel64
cmake ../ -DGMX_FFT_LIBRARY="mkl" -DGMX_GPU=on
-DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
-DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc

It worths to say that the OS under current operation is Lubuntu (16.04)
> and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly
> without problems, however I noticed a std failure after issuing the
> "make" command, it says:
>
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250):
>
> error: namespace "std" has no member "_Exit"
>std:: _Exit(returnValue);
>  ^
>
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251):
>
> warning #1628: function declared with "noreturn" does retu
> rn
>}
>^
>
> The same problem can be seen if I start from a very simple "cmake ../"
> and "make". What am I doing wrong? Is there some environment preparation
> step to be done prior to everything else, and what should it be?
>

On Linux, Intel compilers rely on having and finding a suitable gcc for the
standard library, so I can only presume something is messed up there. For
example, gcc was installed or updated after icc. Try the advice at
http://manual.gromacs.org/documentation/current/install-guide/index.html#compiler

Mark


> I must say that I'm not an expert on compiling things up and I got
> stuck. Could someone help me out? It would be of great help to know some
> tips from you guys.
>
> Thank you all.
>
> Kind regards,
>
> --
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Re: [gmx-users] energy minimization

[farial tavakoli]

 Dear Justin 

Thank you for your reply
I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
named topologen_1.1.pl in the working directory) 
I generated my ligand topology but got this :
No output type specified. Using default type of .top
Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
Using default H type for atom 16.
Using default H type for atom 26.
Using default H type for atom 31.
Using default H type for atom 38.
Using default H type for atom 39.
Using default H type for atom 40.
Using default H type for atom 41.
Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
Using default H type for atom 47.
Using default H type for atom 48.
Using default H type for atom 49.
Using default H type for atom 50.
Using default H type for atom 51.
Using default H type for atom 52.


WARNING: Net charge on the molecule is -2.781
You will need to make corrections to the output topology


TopolGen, version 1.1_dev (10/14/2009) complete.

Output topology has been written. An attempt has been made to assign charges 
and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other 
parameterization calculations have been done.  Guesses have been made for 
charge groups.  Please
inspect and correct the topology before using it in any simulations.  The 
author of the script does 
NOT guarantee accuracy or usability of any of the content; TopolGen was written 
as a convenience 
for outputting a skeleton topology, and nothing more.


the N13 atom connected to C with double bond. it sounds topolgen can not 
identify N atom in 2 bonds with C . 
would you please help me to figure out this problem
thans in advanceFarial

On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/15/18 1:38 AM, farial tavakoli wrote:
>  Dear Justin
>
> But I copied & pasted topolgen and perl5 folders in the working directory. 
> and faced the mentioned error.
>
> Can't open perl script "topolgen.pl": No such file or directory
> I dont know how I should figure out this problem.

The problem is still the same: there's nothing called "topolgen.pl" in 
the working directory. List your files, you'll see it's called something 
else.

> Which one of all-atom force fields will you choose to run a simulation on a 
> complex with small molecule, if you want to calculate binding energy using 
> G_MMPBSA ?I really need your guidance .

Presumably any of them, but I don't do such calculations.

-Justin

-- 
==

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

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

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

==

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Re: [gmx-users] MDRun Compile issue

[Mark Abraham]

Hi,

Please do check out our installation guide... you're doing a few things
that make your life hard and perhaps the resulting simulations slow slow.
http://manual.gromacs.org/documentation/current/install-guide/index.html

On Sun, Jul 15, 2018 at 9:40 PM Weiner, Michael  wrote:

> I am trying to build gromacs 2018.2 on an intel-based HPC that i manage. i
> have the main program built but i want to build MDrun openmp support. I am
> using the latest version of Intel Parallel Studio XE (2018.3) in order to
> compile, as well as the latest boost (1.67.0), gsl (2.5) and openmil
> (3.1.1) sources.


Neither boost or gsl have been dependencies for some years.


> Here is my attemt/configuration to build mdrun with openmpi:
>
>
> -
>
> rm -rf *
> export CC=icc
> export CXX=icpc
>
> export  GROMACS_INSTALL_DIR=/cm/shared/apps/gromacs/2018.2
>
> export
> CMAKE_PREFIX_PATH=/cm/shared/apps/boost/1.67.0:/cm/shared/apps/gsl/2.5
>
> export CFLAGS="-O3 -fast-transcendentals -ftz -fma -fp-model fast=2
> -qopt-calloc  -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp"
>

None of these will help GROMACS, and by using them you risk poor
interactions with those we set that do help. But I don't see any harm,
except that you turned OpenMP support on here, and turned it off below.
Leave OpenMP alone, ie. on by default because it's basically always useful
to users.

export CXXFLAGS=$CFLAGS
> export LDFLAGS=$CFLAGS
>
> export MPICC=mpiicc
>
> cmake \
> -DCMAKE_VERBOSE_MAKEFILE=TRUE \
> -DCMAKE_INSTALL_PREFIX=$GROMACS_INSTALL_DIR \
> -DGMX_GPU=OFF  -DGMX_MPI=ON -DGMX_OPENMP=OFF \
> -DGMX_EXTERNAL_BLAS=OFF \
> -DGMX_BUILD_MDRUN_ONLY=ON \
> -DGMX_FFT_LIBRARY=fftw3  -DGMX_BUILD_OWN_FFTW=ON  .. && make -j25 mdrun &&
> make  install-mdrun
>
>  --
>
>
> It gets 95% of the way through the build and fails with the following:
>
>
> [ 93%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o
> cd /root/temp/gromacs-2018.2/build/src/gromacs &&
> /cm/shared/apps/intel/parallelstudio/2018/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc
> -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -isystem
> /root/temp/gromacs-2018.2/src/external/lmfit
> -I/root/temp/gromacs-2018.2/build/src/contrib/fftw/fftwBuild-prefix/include
> -I/root/temp/gromacs-2018.2/build/src -isystem
> /root/temp/gromacs-2018.2/src/external/thread_mpi/include
> -I/root/temp/gromacs-2018.2/src -isystem
> /cm/shared/apps/openmpi/gcc/64/3.1.1/include
> -I/root/temp/gromacs-2018.2/src/external/tng_io/include
> -I/root/temp/gromacs-2018.2/build/tng/include  -mavx   -O3
> -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc
> -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp -std=c++11
> -wd3180  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias
> -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -o
> CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o -c
> /root/temp/gromacs-2018.2/src/gromacs
>  /mdlib/tpi.cpp
> /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp(2853): error:
> identifier "nthreads" is undefined
>   #pragma omp parallel for num_threads(nthreads) schedule(static)
>^
>
> compilation aborted for
> /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp (code 2)
> make[3]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o] Error 2
>
>
>
> Can anyone provide any insights as to why this is failing and perhaps give
> me some pointers to get it to  compile?
>

Be consistent with your OpenMP options (ie set none of them) and this works.

Mark


>
> Thank you
>
> Michael Weiner
>
> Lead Analyst/UNIX Systems Administrator
>
> Lerner Research Institute Computing Services
>
> Lerner Research Institute
>
> Cleveland Clinic
>
> ===
>
>
>  Please consider the environment before printing this e-mail
>
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> 

Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

[Neda Rafiee]

Dear Mark,
Thanks a lot for your useful suggestions
Neda


- Original Message -
From: Mark Abraham 
To: gmx-us...@gromacs.org
Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT)
Subject: Re: [gmx-users] [Spam-FG]  
[Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

Hi,

I presume that's because you still have interactions between groups that
are frozen.

You can make your life easier by using only the groups you need for your
simulation, e.g. those needing a table and those that are frozen. If you
are trying to get per-residue decomposition, then (first) make sure your
force field was parametrized such that this is meaningful (most aren't),
and prefer to do that analysis using mdrun -rerun. mdrun goes slower for
each energy group that has interactions to compute, so minimize that.

I would also have done a simulation with just my slab and found this
pressure issue back then. It is good practice to add complexity to models
incrementally, after validating your expectations on the simulation at the
previous stage.

Mark

On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee  wrote:

> Dear Justin,
> I added the following energy exclusion pairs to my mdp file. Now potential
> energy decreased significantly but still I have a very large negative
> pressure (minus 10 to power 28) in my system. It seems that pressure is the
> same as before.Should I do anything else?
>
> energygrp-excl= SIB SIB  SIB OXB  SIB OMB  SIB SiSil  SIB OSil  SIB SiGem
> SIB OGem  OXB OXB  OXB OMB  OXB SiSil  OXB OSil  OXB SiGem  OXB OGem  OMB
> OMB  OMB SiSil  OMB OSil  OMB SiGem  OMB OGem  SiSil SiSil  SiSil OSil
> SiSil SiGem  SiSil OGem  OSil OSil  OSil SiGem  OSil OGem  SiGem SiGem
> SiGem OGem  OGem OGem
>
> Thanks
> Neda
>
> - Original Message -
> From: Neda Rafiee 
> To: gmx-us...@gromacs.org
> Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
> Subject: [Spam-FG][gmx-users]
> [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
> http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1
>
> VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBF
>
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> 
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>
> 

Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

[Mark Abraham]

Hi,

I presume that's because you still have interactions between groups that
are frozen.

You can make your life easier by using only the groups you need for your
simulation, e.g. those needing a table and those that are frozen. If you
are trying to get per-residue decomposition, then (first) make sure your
force field was parametrized such that this is meaningful (most aren't),
and prefer to do that analysis using mdrun -rerun. mdrun goes slower for
each energy group that has interactions to compute, so minimize that.

I would also have done a simulation with just my slab and found this
pressure issue back then. It is good practice to add complexity to models
incrementally, after validating your expectations on the simulation at the
previous stage.

Mark

On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee  wrote:

> Dear Justin,
> I added the following energy exclusion pairs to my mdp file. Now potential
> energy decreased significantly but still I have a very large negative
> pressure (minus 10 to power 28) in my system. It seems that pressure is the
> same as before.Should I do anything else?
>
> energygrp-excl= SIB SIB  SIB OXB  SIB OMB  SIB SiSil  SIB OSil  SIB SiGem
> SIB OGem  OXB OXB  OXB OMB  OXB SiSil  OXB OSil  OXB SiGem  OXB OGem  OMB
> OMB  OMB SiSil  OMB OSil  OMB SiGem  OMB OGem  SiSil SiSil  SiSil OSil
> SiSil SiGem  SiSil OGem  OSil OSil  OSil SiGem  OSil OGem  SiGem SiGem
> SiGem OGem  OGem OGem
>
> Thanks
> Neda
>
> - Original Message -
> From: Neda Rafiee 
> To: gmx-us...@gromacs.org
> Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
> Subject: [Spam-FG][gmx-users]
> [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
>
> http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1
>
> VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBF
>
> AfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI
> 
>
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> nAbOD460TYaxz5rvPHU6aKBw_" target="_blank">
> If this email is not spam, click here to submit the signatures to
> FortiGuard - AntiSpam Service.
> 
>
> 
> Dear Justin,
> Thanks a lot for your response.
> Neda
>
> - Original Message -
> From: Justin Lemkul
> To: 

Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

[Neda Rafiee]

Dear Justin,
I added the following energy exclusion pairs to my mdp file. Now potential 
energy decreased significantly but still I have a very large negative pressure 
(minus 10 to power 28) in my system. It seems that pressure is the same as 
before.Should I do anything else?

energygrp-excl= SIB SIB  SIB OXB  SIB OMB  SIB SiSil  SIB OSil  SIB SiGem  SIB 
OGem  OXB OXB  OXB OMB  OXB SiSil  OXB OSil  OXB SiGem  OXB OGem  OMB OMB  OMB 
SiSil  OMB OSil  OMB SiGem  OMB OGem  SiSil SiSil  SiSil OSil  SiSil SiGem  
SiSil OGem  OSil OSil  OSil SiGem  OSil OGem  SiGem SiGem  SiGem OGem  OGem OGem

Thanks
Neda

- Original Message -
From: Neda Rafiee 
To: gmx-us...@gromacs.org
Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
Subject: [Spam-FG][gmx-users] 
[Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

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Dear Justin,
Thanks a lot for your response.
Neda

- Original Message -
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Sent: Sun, 15 Jul 2018 23:09:11 +0430 (IRDT)
Subject: [Spam-FG] Re: [gmx-users] Negative pressure in NVT simulation



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On 7/15/18 2:32 PM, Neda Rafiee wrote:
 ;
 energygrps  = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil 
OGem OMB SIB SiSil SiGem HSil HGem OW HW
 energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil 
OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW

 freezegrps  = SIB OXB OMB SiSil OSil SiGem OGem
 freezedim   = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y

Youre not using energy group