[gmx-users] free energy calculations

2016-01-29 Thread Marta Wisniewska 
Dear Gromac's users,

I'd like to perform a FEP calculations. I've done yours tutorial and now
follow by it, i'd like to perform my calculations for small molecule in
water. I got a problem:
Fatal error:
No such moleculetype SOL

I don't know what it means in these cases, because both files are similar
to each other (yours and mine).

Co you have any idea?
thank you in advance,
Marta
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Re: [gmx-users] (no subject)

2016-01-29 Thread Justin Lemkul 



On 1/29/16 8:10 AM, Sepideh Momeninezhad wrote:

hi
I am a new user of gromacs i need a tutorial to study the interaction
between two molecule,please tell me where I can find it!



Tutorials are listed on the GROMACS website or via your own search via Google. 
Note that "two molecules" is ambiguous; any MD simulation will have more than 
two molecules, but what are they?  Two proteins?  Two water molecules?  Big 
difference.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] (no subject)

2016-01-29 Thread Sepideh Momeninezhad 
thanks for your answer.
I want to simulate DNA and peptide nucleic acid.
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Re: [gmx-users] free energy calculations

2016-01-29 Thread Justin Lemkul 



On 1/29/16 7:27 AM, Marta Wisniewska wrote:

Dear Gromac's users,

I'd like to perform a FEP calculations. I've done yours tutorial and now
follow by it, i'd like to perform my calculations for small molecule in
water. I got a problem:
Fatal error:
No such moleculetype SOL

I don't know what it means in these cases, because both files are similar
to each other (yours and mine).



The error means you haven't defined the water topology, or for whatever reason 
your water has a different [moleculetype] name.


Please note there are several GROMACS free energy tutorials online; if you're 
trying to compare with one of those, please state which one you're using.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] (no subject)

2016-01-29 Thread Sepideh Momeninezhad 
hi
I am a new user of gromacs i need a tutorial to study the interaction
between two molecule,please tell me where I can find it!
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Re: [gmx-users] free energy calculations

2016-01-29 Thread Stefania Evoli 
Dear Marta,

Probably you forgot to put the line regarding the topology of the water
into the topology file of your system.

#include "amber99sb.ff/tip3p.itp² (for example)


Stefania


‹Dr. Stefania Evoli
Post-Doctoral Fellow
King Abdullah University of Science and Technology
Catalysis center - Bldg. 3, 4th floor, 4231­WS18
Thuwal, Kingdom of Saudi Arabia
stefania.ev...@kaust.edu.sa






On 1/29/16, 3:27 PM, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Marta Wisniewska"
 wrote:

>Dear Gromac's users,
>
>I'd like to perform a FEP calculations. I've done yours tutorial and now
>follow by it, i'd like to perform my calculations for small molecule in
>water. I got a problem:
>Fatal error:
>No such moleculetype SOL
>
>I don't know what it means in these cases, because both files are similar
>to each other (yours and mine).
>
>Co you have any idea?
>thank you in advance,
>Marta
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>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
>
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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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[gmx-users] add new residue and new atom

2016-01-29 Thread Malihe Hasanzadeh 
Hi

I used a PDB structure for MD simulation which it has a carbamylated Lys
(KCX 220). This residue via carbamyl group bonded to metal in active site.
So I had to define new residue(KCX), I copied parameters of Lys residue and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
   [ KCX ]
 [ atoms ]
 NN   -0.34790 1
 HH0.27470 2
CACT  -0.24000 3
HAH1   0.14260 4
CBCT  -0.00940 5
   HB1HC   0.03620 6
   HB2HC   0.03620 7
CGCT   0.01870 8
   HG1HC   0.01030 9
   HG2HC   0.0103010
CDCT  -0.0479011
   HD1HC   0.0621012
   HD2HC   0.0621013
CECT  -0.0143014
   HE1HP   0.1135015
   HE2HP   0.1135016
NZN3  -0.3854017
   HZ1H0.3400018
   HZ2H0.3400019
   HZ3H0.3400020
 CC0.7341021
 OO   -0.5894022
CXC0.7341023
HXH0.2747024
   OQ1O   -0.5894025
   OQ2O   -0.5894026
 [ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGCD
CD   HD1
CD   HD2
CDCE
CE   HE1
CE   HE2
CENZ
NZ   HZ1
NZ   HZ2
NZ   HZ3
NZCX
 C O
-C N
CX   OQ1
CX   OQ2
CXHX
 [ impropers ]
-CCA N H
CA+N C O
NZ   OQ1CX   OQ2

In addition this protein has two Ni ion, that I added its parameters in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after energy
minimization, I extract em.pdb file and I saw the distance between NI ion
in active site with F ion in ligand is much more ( ~5 A) than before in
complex.pdb. This means my ligand isn't stable in active site and it is
moving away!

please help me. what is my mistake?why ligand moving away and why gromacs
doesn't identify end of the protein? Is there a relationship between added
parameters and getting away of ligand?

Thanks
Malihe
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[gmx-users] error about x of the xxx bonded interactions could not be calculated ....

2016-01-29 Thread Chang Woon Jang 
Dear Gromacs Users,

   I am simulating coarse grained polymer systems with tabulated potential
(A B C D types).

To obtain pair potentials, Iterative Boltzmann Inversion is used with
Gromacs.

After 14 step (each step runs 1 ns (100) with time step 1 fs - 0.001),
the simulation had failed with the following error.

x of xxx bonded interactions could not be calculated 

It sounds like Blowing Up problem. Therefore, I reduced the time step to
0.0008 (0.8 fs), then the simulation failed at 164 step.

I do not think that I started 1) a bad structure due to I equilibrated for
120 ns at atomistic level, 2) inappropriate pressure coupling because I use
NVT ensemble.

I am not sure what the following tip is in the gromacs website.

"*your position restraints are to coordinates too different from those
present in the system,*"


I am using gromacs 5.0.8-dev-20151014-1f04b58

Do you have any advice for solving this problem?

I still keep decreasing the time step now at 0.0006.

Thank you.


Best regards,
Changwoon Jang,
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Re: [gmx-users] error about x of the xxx bonded interactions could not be calculated ....

2016-01-29 Thread Mark Abraham 
Hi,

You should verify that your tables implement the model you think they do.
Use http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
calculations on two-particle systems to verify you can reproduce trivial
energies and forces.

Mark

On Fri, 29 Jan 2016 17:17 Chang Woon Jang  wrote:

> Dear Gromacs Users,
>
>I am simulating coarse grained polymer systems with tabulated potential
> (A B C D types).
>
> To obtain pair potentials, Iterative Boltzmann Inversion is used with
> Gromacs.
>
> After 14 step (each step runs 1 ns (100) with time step 1 fs - 0.001),
> the simulation had failed with the following error.
>
> x of xxx bonded interactions could not be calculated 
>
> It sounds like Blowing Up problem. Therefore, I reduced the time step to
> 0.0008 (0.8 fs), then the simulation failed at 164 step.
>
> I do not think that I started 1) a bad structure due to I equilibrated for
> 120 ns at atomistic level, 2) inappropriate pressure coupling because I use
> NVT ensemble.
>
> I am not sure what the following tip is in the gromacs website.
>
> "*your position restraints are to coordinates too different from those
> present in the system,*"
>
>
> I am using gromacs 5.0.8-dev-20151014-1f04b58
>
> Do you have any advice for solving this problem?
>
> I still keep decreasing the time step now at 0.0006.
>
> Thank you.
>
>
> Best regards,
> Changwoon Jang,
> --
> 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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Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Justin Lemkul 



On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:

Hi

I used a PDB structure for MD simulation which it has a carbamylated Lys
(KCX 220). This residue via carbamyl group bonded to metal in active site.
So I had to define new residue(KCX), I copied parameters of Lys residue and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
[ KCX ]
  [ atoms ]
  NN   -0.34790 1
  HH0.27470 2
 CACT  -0.24000 3
 HAH1   0.14260 4
 CBCT  -0.00940 5
HB1HC   0.03620 6
HB2HC   0.03620 7
 CGCT   0.01870 8
HG1HC   0.01030 9
HG2HC   0.0103010
 CDCT  -0.0479011
HD1HC   0.0621012
HD2HC   0.0621013
 CECT  -0.0143014
HE1HP   0.1135015
HE2HP   0.1135016
 NZN3  -0.3854017
HZ1H0.3400018
HZ2H0.3400019
HZ3H0.3400020
  CC0.7341021
  OO   -0.5894022
 CXC0.7341023
 HXH0.2747024
OQ1O   -0.5894025
OQ2O   -0.5894026
  [ bonds ]
  N H
  NCA
 CAHA
 CACB
 CA C
 CB   HB1
 CB   HB2
 CBCG
 CG   HG1
 CG   HG2
 CGCD
 CD   HD1
 CD   HD2
 CDCE
 CE   HE1
 CE   HE2
 CENZ
 NZ   HZ1
 NZ   HZ2
 NZ   HZ3
 NZCX
  C O
 -C N
 CX   OQ1
 CX   OQ2
 CXHX
  [ impropers ]
 -CCA N H
 CA+N C O
 NZ   OQ1CX   OQ2

In addition this protein has two Ni ion, that I added its parameters in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after energy
minimization, I extract em.pdb file and I saw the distance between NI ion
in active site with F ion in ligand is much more ( ~5 A) than before in
complex.pdb. This means my ligand isn't stable in active site and it is
moving away!

please help me. what is my mistake?why ligand moving away and why gromacs
doesn't identify end of the protein? Is there a relationship between added
parameters and getting away of ligand?



You forgot step 5: 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field


pdb2gmx writes your custom residue as its own chain, not bonded to the rest of 
the protein, so it is its own separate molecule.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] add new residue and new atom

2016-01-29 Thread Malihe Hasanzadeh 
Hi

I used a PDB structure for MD simulation which it has a carbamylated Lys
(KCX 220). This residue via carbamyl group bonded to metal in active site.
So I had to define new residue(KCX), I copied parameters of Lys residue and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
   [ KCX ]
 [ atoms ]
 NN   -0.34790 1
 HH0.27470 2
CACT  -0.24000 3
HAH1   0.14260 4
CBCT  -0.00940 5
   HB1HC   0.03620 6
   HB2HC   0.03620 7
CGCT   0.01870 8
   HG1HC   0.01030 9
   HG2HC   0.0103010
CDCT  -0.0479011
   HD1HC   0.0621012
   HD2HC   0.0621013
CECT  -0.0143014
   HE1HP   0.1135015
   HE2HP   0.1135016
NZN3  -0.3854017
   HZ1H0.3400018
   HZ2H0.3400019
   HZ3H0.3400020
 CC0.7341021
 OO   -0.5894022
CXC0.7341023
HXH0.2747024
   OQ1O   -0.5894025
   OQ2O   -0.5894026
 [ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGCD
CD   HD1
CD   HD2
CDCE
CE   HE1
CE   HE2
CENZ
NZ   HZ1
NZ   HZ2
NZ   HZ3
NZCX
 C O
-C N
CX   OQ1
CX   OQ2
CXHX
 [ impropers ]
-CCA N H
CA+N C O
NZ   OQ1CX   OQ2

In addition this protein has two Ni ion, that I added its parameters in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after energy
minimization, I extract em.pdb file and I saw the distance between NI ion
in active site with F ion in ligand is much more ( ~5 A) than before in
complex.pdb. This means my ligand isn't stable in active site and it is
moving away!

please help me. what is my mistake?why ligand moving away and why gromacs
doesn't identify end of the protein? Is there a relationship between added
parameters and getting away of ligand?

Thanks
-- 
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] error about x of the xxx bonded interactions could not be calculated ....

2016-01-29 Thread Chang Woon Jang 
Dear Mark Abraham,

   Thank you for your advice.

When I did "mdrun -s topol.tpr -rerun conf.gro", the following warnings are
present.


Do you think that this is the problem? I have two tabulated bond potentials
(A-B, C-D) and two tabulated angle potentials (A-B-A, C-D-C). As you can
see, the only table_b1.xvg produced the warnings.

Does this mean that table_b1.xvg (A-B bonded potential) led the simulation
failure somehow?

Thank you.

Best regards,
Changwoon Jang

=

WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting md rerun 'Built with Packmol', reading coordinates from input
trajectory 'confout.gro'

Reading frames from gro file 'Built with Packmol', 900 atoms.
Last frame  0 time0.000

NOTE: 10 % of the run time was spent communicating energies,
  you might want to use the -gcom option of mdrun


   Core t (s)   Wall t (s)(%)
   Time:0.0480.020  239.1
 (ns/day)(hour/ns)
Performance:3.4336.991

gcq#10: "Bum Stikkie Di Bum Stikkie Di Bum Stikkie Di Bum" (R. Slijngaard)



On Fri, Jan 29, 2016 at 11:27 AM, Mark Abraham 
wrote:

> Hi,
>
> You should verify that your tables implement the model you think they do.
> Use http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> calculations on two-particle systems to verify you can reproduce trivial
> energies and forces.
>
> Mark
>
> On Fri, 29 Jan 2016 17:17 Chang Woon Jang  wrote:
>
> > Dear Gromacs Users,
> >
> >I am simulating coarse grained polymer systems with tabulated
> potential
> > (A B C D types).
> >
> > To obtain pair potentials, Iterative Boltzmann Inversion is used with
> > Gromacs.
> >
> > After 14 step (each step runs 1 ns (100) with time step 1 fs -
> 0.001),
> > the simulation had failed with the following error.
> >
> > x of xxx bonded interactions could not be calculated 
> >
> > It sounds like Blowing Up problem. Therefore, I reduced the time step to
> > 0.0008 (0.8 fs), then the simulation failed at 164 step.
> >
> > I do not think that I started 1) a bad structure due to I equilibrated
> for
> > 120 ns at atomistic level, 2) inappropriate pressure coupling because I
> use
> > NVT ensemble.
> >
> > I am not sure what the following tip is in the gromacs website.
> >
> > "*your position restraints are to coordinates too different from those
> > present in the system,*"
> >
> >
> > I am using gromacs 5.0.8-dev-20151014-1f04b58
> >
> > Do you have any advice for solving this problem?
> >
> > I still keep decreasing the time step now at 0.0006.
> >
> > Thank you.
> >
> >
> > Best regards,
> > Changwoon Jang,
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267

Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Justin Lemkul 



On 1/29/16 12:22 PM, Malihe Hasanzadeh wrote:

Dear Justin,
Is there any way to get parameters of KCX residue for amber99sb-ildn?


Well, how did you get the ones you have?  And are you familiar with what the 
differences are between AMBER99sb and AMBER99sb-ILDN?


-Justin


Thanks
Malihe

On Fri, Jan 29, 2016 at 8:45 PM, Justin Lemkul  wrote:




On 1/29/16 12:13 PM, Malihe Hasanzadeh wrote:


Dear justin,
I forgot to write this step here, but I did this step also. I added (KCX
Protein) in .dat file. But unfortunately as you say the gromacs dosen't
identify my new residue!



If this were true, pdb2gmx would not tell you otherwise.  You didn't do
what you thought you did, or you modified the wrong files.

What should I do? Is my added parameters for KCX residue correct?




Follow the steps exactly in the link I provided.  That's all there is to
it.

-Justin

Thanks

Malihe

On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul  wrote:




On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:

Hi


I used a PDB structure for MD simulation which it has a carbamylated Lys
(KCX 220). This residue via carbamyl group bonded to metal in active
site.
So I had to define new residue(KCX), I copied parameters of Lys residue
and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
  [ KCX ]
[ atoms ]
NN   -0.34790 1
HH0.27470 2
   CACT  -0.24000 3
   HAH1   0.14260 4
   CBCT  -0.00940 5
  HB1HC   0.03620 6
  HB2HC   0.03620 7
   CGCT   0.01870 8
  HG1HC   0.01030 9
  HG2HC   0.0103010
   CDCT  -0.0479011
  HD1HC   0.0621012
  HD2HC   0.0621013
   CECT  -0.0143014
  HE1HP   0.1135015
  HE2HP   0.1135016
   NZN3  -0.3854017
  HZ1H0.3400018
  HZ2H0.3400019
  HZ3H0.3400020
CC0.7341021
OO   -0.5894022
   CXC0.7341023
   HXH0.2747024
  OQ1O   -0.5894025
  OQ2O   -0.5894026
[ bonds ]
N H
NCA
   CAHA
   CACB
   CA C
   CB   HB1
   CB   HB2
   CBCG
   CG   HG1
   CG   HG2
   CGCD
   CD   HD1
   CD   HD2
   CDCE
   CE   HE1
   CE   HE2
   CENZ
   NZ   HZ1
   NZ   HZ2
   NZ   HZ3
   NZCX
C O
   -C N
   CX   OQ1
   CX   OQ2
   CXHX
[ impropers ]
   -CCA N H
   CA+N C O
   NZ   OQ1CX   OQ2

In addition this protein has two Ni ion, that I added its parameters in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it
closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from
starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from
starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified
residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after
energy
minimization, I extract em.pdb file and I saw the distance between NI
ion
in active site with F ion in ligand is much more ( ~5 A) than before in
complex.pdb. This means my ligand isn't stable in active site and it is
moving away!

please help me. what is my mistake?why ligand moving away and why
gromacs
doesn't identify end of the protein? Is there a relationship between
added
parameters and getting away of ligand?


You forgot step 5:


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

pdb2gmx writes your custom residue as its own chain, not bonded to the
rest of the protein, so it is its own separate molecule.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health

Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Justin Lemkul 



On 1/29/16 12:49 PM, Malihe Hasanzadeh wrote:

Dear Justin,
I know these Force fields as much as I can use them. I use always
AMBER99sb-ILDN in my simulations actually like this time, but I'm sorry for
notify name of force field as incomplete. I copied parameters of Lys
residue from .rtp file in AMBER99sb-ILDN for my new residue (KCX) and only
data of carbamyl group added to it (below) as I said before.
CX   OQ1
CX   OQ2
CXHX


You have a simple issue of an absent assignment of residue type in 
residuetypes.dat that triggers this problem.  I don't know why we're re-hashing 
the details of an .rtp entry that has already been constructed.  That's not your 
problem.


-Justin


Malihe

On Fri, Jan 29, 2016 at 8:54 PM, Justin Lemkul  wrote:




On 1/29/16 12:22 PM, Malihe Hasanzadeh wrote:


Dear Justin,
Is there any way to get parameters of KCX residue for amber99sb-ildn?



Well, how did you get the ones you have?  And are you familiar with what
the differences are between AMBER99sb and AMBER99sb-ILDN?

-Justin

Thanks

Malihe

On Fri, Jan 29, 2016 at 8:45 PM, Justin Lemkul  wrote:




On 1/29/16 12:13 PM, Malihe Hasanzadeh wrote:

Dear justin,

I forgot to write this step here, but I did this step also. I added (KCX
Protein) in .dat file. But unfortunately as you say the gromacs dosen't
identify my new residue!



If this were true, pdb2gmx would not tell you otherwise.  You didn't do
what you thought you did, or you modified the wrong files.

What should I do? Is my added parameters for KCX residue correct?





Follow the steps exactly in the link I provided.  That's all there is to
it.

-Justin

Thanks


Malihe

On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul  wrote:




On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:

Hi



I used a PDB structure for MD simulation which it has a carbamylated
Lys
(KCX 220). This residue via carbamyl group bonded to metal in active
site.
So I had to define new residue(KCX), I copied parameters of Lys
residue
and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
   [ KCX ]
 [ atoms ]
 NN   -0.34790 1
 HH0.27470 2
CACT  -0.24000 3
HAH1   0.14260 4
CBCT  -0.00940 5
   HB1HC   0.03620 6
   HB2HC   0.03620 7
CGCT   0.01870 8
   HG1HC   0.01030 9
   HG2HC   0.0103010
CDCT  -0.0479011
   HD1HC   0.0621012
   HD2HC   0.0621013
CECT  -0.0143014
   HE1HP   0.1135015
   HE2HP   0.1135016
NZN3  -0.3854017
   HZ1H0.3400018
   HZ2H0.3400019
   HZ3H0.3400020
 CC0.7341021
 OO   -0.5894022
CXC0.7341023
HXH0.2747024
   OQ1O   -0.5894025
   OQ2O   -0.5894026
 [ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGCD
CD   HD1
CD   HD2
CDCE
CE   HE1
CE   HE2
CENZ
NZ   HZ1
NZ   HZ2
NZ   HZ3
NZCX
 C O
-C N
CX   OQ1
CX   OQ2
CXHX
 [ impropers ]
-CCA N H
CA+N C O
NZ   OQ1CX   OQ2

In addition this protein has two Ni ion, that I added its parameters
in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it
closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation
I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from
starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from
starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified
residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after
energy
minimization, I

[gmx-users] Heat capacity (C_{v}) for a solid

2016-01-29 Thread Alexander Alexander 
Dear Gromacs user,

I am trying to calculate the heat capacity at constant volume (C_{v}) in
different temperature for a solid structure with "A_{3}B" chemical formula.
To do so, I made a big supercell containing totally "43904" atom by keeping
the rate (#A = 32928 and #B=10976), below is a part of my topology file.
topol.top:
-
[ moleculetype ]
; Namenrexcl
  A   1

[ moleculetype ]
; Namenrexcl
  B1

[ molecules ]
;mol_name number
   A32928
   B 10976
-

After convergence of the MD simulation I invoked the below command:

"gmx energy -f case.edr -nmol 43904 -fluct_props -o case.xvg"

My first question:
what exactly I should use as "-nmol" in this specific case as explained
above? If it is (#A) or (#B) or (#A+#B)?

Second question:
I was wondering if the Cv printed out in screen after choosing "Total
Energy"  and "Temperature" in gmx energy is relabel?  At least in this
level as I know the Quantum part has not been included yet.  Or I have to
do the temperature numerical derivation of Total energy myself as
Cv=d(U)/d(T).

WARNING: Please verify that your simulations are converged and perform
a block-averaging error analysis (not implemented in g_energy yet)
Heat capacity at constant volume Cv   =200.779 J/mol K.

Third question:
If this is Molar heat capacity, am I right?

The last:
Below are the result of Cv in different temperature for this system:

(Cv  J/mol K) - (Temperature K)
37037.700  10
 200.779  50
   40.497  75
 124.360  100
 321.416  150
 620.247  298

I know these Cv do not include any corrections for quantum yet, but still I
am puzzled about the strange behavior of  Cv versus temperature, I would be
so thankful if one could explain it for me.

(Version of Gromacs : is 5.1-rc1)

Sincerely,

Alex
-- 
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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Re: [gmx-users] error about x of the xxx bonded interactions could not be calculated ....

2016-01-29 Thread Mark Abraham 
Hi,

That seems extremely likely. Prove your tables work on something trivially
simple.

Mark

On Fri, 29 Jan 2016 17:51 Chang Woon Jang  wrote:

> Dear Mark Abraham,
>
>Thank you for your advice.
>
> When I did "mdrun -s topol.tpr -rerun conf.gro", the following warnings are
> present.
>
>
> Do you think that this is the problem? I have two tabulated bond potentials
> (A-B, C-D) and two tabulated angle potentials (A-B-A, C-D-C). As you can
> see, the only table_b1.xvg produced the warnings.
>
> Does this mean that table_b1.xvg (A-B bonded potential) led the simulation
> failure somehow?
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> =
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
> forces deviate on average 179% from minus the numerical derivative of the
> potential
>
>
> Back Off! I just backed up ener.edr to ./#ener.edr.2#
> starting md rerun 'Built with Packmol', reading coordinates from input
> trajectory 'confout.gro'
>
> Reading frames from gro file 'Built with Packmol', 900 atoms.
> Last frame  0 time0.000
>
> NOTE: 10 % of the run time was spent communicating energies,
>   you might want to use the -gcom option of mdrun
>
>
>Core t (s)   Wall t (s)(%)
>Time:0.0480.020  239.1
>  (ns/day)(hour/ns)
> Performance:3.4336.991
>
> gcq#10: "Bum Stikkie Di Bum Stikkie Di Bum Stikkie Di Bum" (R. Slijngaard)
>
>
>
> On Fri, Jan 29, 2016 at 11:27 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You should verify that your tables implement the model you think they do.
> > Use http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> > calculations on two-particle systems to verify you can reproduce trivial
> > energies and forces.
> >
> > Mark
> >
> > On Fri, 29 Jan 2016 17:17 Chang Woon Jang 
> wrote:
> >
> > > Dear Gromacs Users,
> > >
> > >I am simulating coarse grained polymer systems with tabulated
> > potential
> > > (A B C D types).
> > >
> > > To obtain pair potentials, Iterative Boltzmann Inversion is used with
> > > Gromacs.
> > >
> > > After 14 step (each step runs 1 ns (100) with time step 1 fs -
> > 0.001),
> > > the simulation had failed with the following error.
> > >
> > > x of xxx bonded interactions could not be calculated 
> > >
> > > It sounds like Blowing Up problem. Therefore, I reduced the time step
> to
> > > 0.0008 (0.8 fs), then the simulation failed at 164 step.
> > >
> > > I do not think that I started 1) a bad structure due to I equilibrated
> > for
> > > 120 ns at atomistic level, 2) inappropriate pressure coupling because I
> > use
> > > NVT ensemble.
> > >
> > > I am not sure what the following tip is in the gromacs website.
> > >
> > > "*your position restraints are to coordinates too different from those
> > > present in the system,*"
> > >
> > >
> > > I am using gromacs 5.0.8-dev-20151014-1f04b58
> > >
> > > Do you have any advice for solving this problem?
> > >
> > > I still keep decreasing the time step now at 0.0006.
> > >
> > > Thank you.
> > >
> > >
> > > Best regards,
> > > Changwoon Jang,
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Justin Lemkul 



On 1/29/16 12:13 PM, Malihe Hasanzadeh wrote:

Dear justin,
I forgot to write this step here, but I did this step also. I added (KCX
Protein) in .dat file. But unfortunately as you say the gromacs dosen't
identify my new residue!


If this were true, pdb2gmx would not tell you otherwise.  You didn't do what you 
thought you did, or you modified the wrong files.



What should I do? Is my added parameters for KCX residue correct?


Follow the steps exactly in the link I provided.  That's all there is to it.

-Justin


Thanks
Malihe

On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul  wrote:




On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:


Hi

I used a PDB structure for MD simulation which it has a carbamylated Lys
(KCX 220). This residue via carbamyl group bonded to metal in active site.
So I had to define new residue(KCX), I copied parameters of Lys residue
and
added carbamyl group and added to .rtp file in amber force field
(99sb)(gromacs5.0.4). I bring KCX parameters in below:
 [ KCX ]
   [ atoms ]
   NN   -0.34790 1
   HH0.27470 2
  CACT  -0.24000 3
  HAH1   0.14260 4
  CBCT  -0.00940 5
 HB1HC   0.03620 6
 HB2HC   0.03620 7
  CGCT   0.01870 8
 HG1HC   0.01030 9
 HG2HC   0.0103010
  CDCT  -0.0479011
 HD1HC   0.0621012
 HD2HC   0.0621013
  CECT  -0.0143014
 HE1HP   0.1135015
 HE2HP   0.1135016
  NZN3  -0.3854017
 HZ1H0.3400018
 HZ2H0.3400019
 HZ3H0.3400020
   CC0.7341021
   OO   -0.5894022
  CXC0.7341023
  HXH0.2747024
 OQ1O   -0.5894025
 OQ2O   -0.5894026
   [ bonds ]
   N H
   NCA
  CAHA
  CACB
  CA C
  CB   HB1
  CB   HB2
  CBCG
  CG   HG1
  CG   HG2
  CGCD
  CD   HD1
  CD   HD2
  CDCE
  CE   HE1
  CE   HE2
  CENZ
  NZ   HZ1
  NZ   HZ2
  NZ   HZ3
  NZCX
   C O
  -C N
  CX   OQ1
  CX   OQ2
  CXHX
   [ impropers ]
  -CCA N H
  CA+N C O
  NZ   OQ1CX   OQ2

In addition this protein has two Ni ion, that I added its parameters in
.atp .itp and .dat files.
Also my ligand has a F ion that when I docked with the protein, it closed
to Ni ion in active site (distance 2.9 A). when I start MD simulation I
faced with two problems:

1. when I run pdb2gmx gives many warning:

Identified residue MET1 as a starting terminus.
Warning: Residue KCX220 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ILE221 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue HIS222 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue GLU223 in chain has different type (Protein) from
starting
residue MET1 (Protein).
Warning: Residue ASP224 in chain has different type (Protein) from
starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue LEU219 as a ending terminus.

My protein has 570 residue, but as you see the gromacs identified residue
LEU219 as a ending terminus.!

2. when I used -missing option and continued my simulations, after energy
minimization, I extract em.pdb file and I saw the distance between NI ion
in active site with F ion in ligand is much more ( ~5 A) than before in
complex.pdb. This means my ligand isn't stable in active site and it is
moving away!

please help me. what is my mistake?why ligand moving away and why gromacs
doesn't identify end of the protein? Is there a relationship between added
parameters and getting away of ligand?



You forgot step 5:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

pdb2gmx writes your custom residue as its own chain, not bonded to the
rest of the protein, so it is its own separate molecule.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read

Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Malihe Hasanzadeh 
Dear justin,
I forgot to write this step here, but I did this step also. I added (KCX
Protein) in .dat file. But unfortunately as you say the gromacs dosen't
identify my new residue!
What should I do? Is my added parameters for KCX residue correct?
Thanks
Malihe

On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul  wrote:

>
>
> On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:
>
>> Hi
>>
>> I used a PDB structure for MD simulation which it has a carbamylated Lys
>> (KCX 220). This residue via carbamyl group bonded to metal in active site.
>> So I had to define new residue(KCX), I copied parameters of Lys residue
>> and
>> added carbamyl group and added to .rtp file in amber force field
>> (99sb)(gromacs5.0.4). I bring KCX parameters in below:
>> [ KCX ]
>>   [ atoms ]
>>   NN   -0.34790 1
>>   HH0.27470 2
>>  CACT  -0.24000 3
>>  HAH1   0.14260 4
>>  CBCT  -0.00940 5
>> HB1HC   0.03620 6
>> HB2HC   0.03620 7
>>  CGCT   0.01870 8
>> HG1HC   0.01030 9
>> HG2HC   0.0103010
>>  CDCT  -0.0479011
>> HD1HC   0.0621012
>> HD2HC   0.0621013
>>  CECT  -0.0143014
>> HE1HP   0.1135015
>> HE2HP   0.1135016
>>  NZN3  -0.3854017
>> HZ1H0.3400018
>> HZ2H0.3400019
>> HZ3H0.3400020
>>   CC0.7341021
>>   OO   -0.5894022
>>  CXC0.7341023
>>  HXH0.2747024
>> OQ1O   -0.5894025
>> OQ2O   -0.5894026
>>   [ bonds ]
>>   N H
>>   NCA
>>  CAHA
>>  CACB
>>  CA C
>>  CB   HB1
>>  CB   HB2
>>  CBCG
>>  CG   HG1
>>  CG   HG2
>>  CGCD
>>  CD   HD1
>>  CD   HD2
>>  CDCE
>>  CE   HE1
>>  CE   HE2
>>  CENZ
>>  NZ   HZ1
>>  NZ   HZ2
>>  NZ   HZ3
>>  NZCX
>>   C O
>>  -C N
>>  CX   OQ1
>>  CX   OQ2
>>  CXHX
>>   [ impropers ]
>>  -CCA N H
>>  CA+N C O
>>  NZ   OQ1CX   OQ2
>>
>> In addition this protein has two Ni ion, that I added its parameters in
>> .atp .itp and .dat files.
>> Also my ligand has a F ion that when I docked with the protein, it closed
>> to Ni ion in active site (distance 2.9 A). when I start MD simulation I
>> faced with two problems:
>>
>> 1. when I run pdb2gmx gives many warning:
>>
>> Identified residue MET1 as a starting terminus.
>> Warning: Residue KCX220 in chain has different type (Other) from starting
>> residue MET1 (Protein).
>> Warning: Residue ILE221 in chain has different type (Protein) from
>> starting
>> residue MET1 (Protein).
>> Warning: Residue HIS222 in chain has different type (Protein) from
>> starting
>> residue MET1 (Protein).
>> Warning: Residue GLU223 in chain has different type (Protein) from
>> starting
>> residue MET1 (Protein).
>> Warning: Residue ASP224 in chain has different type (Protein) from
>> starting
>> residue MET1 (Protein).
>> More than 5 unidentified residues at end of chain - disabling further
>> warnings.
>> Identified residue LEU219 as a ending terminus.
>>
>> My protein has 570 residue, but as you see the gromacs identified residue
>> LEU219 as a ending terminus.!
>>
>> 2. when I used -missing option and continued my simulations, after energy
>> minimization, I extract em.pdb file and I saw the distance between NI ion
>> in active site with F ion in ligand is much more ( ~5 A) than before in
>> complex.pdb. This means my ligand isn't stable in active site and it is
>> moving away!
>>
>> please help me. what is my mistake?why ligand moving away and why gromacs
>> doesn't identify end of the protein? Is there a relationship between added
>> parameters and getting away of ligand?
>>
>>
> You forgot step 5:
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> pdb2gmx writes your custom residue as its own chain, not bonded to the
> rest of the protein, so it is its own separate molecule.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> *

Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Malihe Hasanzadeh 
Dear Justin,
Is there any way to get parameters of KCX residue for amber99sb-ildn?
Thanks
Malihe

On Fri, Jan 29, 2016 at 8:45 PM, Justin Lemkul  wrote:

>
>
> On 1/29/16 12:13 PM, Malihe Hasanzadeh wrote:
>
>> Dear justin,
>> I forgot to write this step here, but I did this step also. I added (KCX
>> Protein) in .dat file. But unfortunately as you say the gromacs dosen't
>> identify my new residue!
>>
>
> If this were true, pdb2gmx would not tell you otherwise.  You didn't do
> what you thought you did, or you modified the wrong files.
>
> What should I do? Is my added parameters for KCX residue correct?
>>
>
> Follow the steps exactly in the link I provided.  That's all there is to
> it.
>
> -Justin
>
> Thanks
>> Malihe
>>
>> On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:
>>>
>>> Hi

 I used a PDB structure for MD simulation which it has a carbamylated Lys
 (KCX 220). This residue via carbamyl group bonded to metal in active
 site.
 So I had to define new residue(KCX), I copied parameters of Lys residue
 and
 added carbamyl group and added to .rtp file in amber force field
 (99sb)(gromacs5.0.4). I bring KCX parameters in below:
  [ KCX ]
[ atoms ]
NN   -0.34790 1
HH0.27470 2
   CACT  -0.24000 3
   HAH1   0.14260 4
   CBCT  -0.00940 5
  HB1HC   0.03620 6
  HB2HC   0.03620 7
   CGCT   0.01870 8
  HG1HC   0.01030 9
  HG2HC   0.0103010
   CDCT  -0.0479011
  HD1HC   0.0621012
  HD2HC   0.0621013
   CECT  -0.0143014
  HE1HP   0.1135015
  HE2HP   0.1135016
   NZN3  -0.3854017
  HZ1H0.3400018
  HZ2H0.3400019
  HZ3H0.3400020
CC0.7341021
OO   -0.5894022
   CXC0.7341023
   HXH0.2747024
  OQ1O   -0.5894025
  OQ2O   -0.5894026
[ bonds ]
N H
NCA
   CAHA
   CACB
   CA C
   CB   HB1
   CB   HB2
   CBCG
   CG   HG1
   CG   HG2
   CGCD
   CD   HD1
   CD   HD2
   CDCE
   CE   HE1
   CE   HE2
   CENZ
   NZ   HZ1
   NZ   HZ2
   NZ   HZ3
   NZCX
C O
   -C N
   CX   OQ1
   CX   OQ2
   CXHX
[ impropers ]
   -CCA N H
   CA+N C O
   NZ   OQ1CX   OQ2

 In addition this protein has two Ni ion, that I added its parameters in
 .atp .itp and .dat files.
 Also my ligand has a F ion that when I docked with the protein, it
 closed
 to Ni ion in active site (distance 2.9 A). when I start MD simulation I
 faced with two problems:

 1. when I run pdb2gmx gives many warning:

 Identified residue MET1 as a starting terminus.
 Warning: Residue KCX220 in chain has different type (Other) from
 starting
 residue MET1 (Protein).
 Warning: Residue ILE221 in chain has different type (Protein) from
 starting
 residue MET1 (Protein).
 Warning: Residue HIS222 in chain has different type (Protein) from
 starting
 residue MET1 (Protein).
 Warning: Residue GLU223 in chain has different type (Protein) from
 starting
 residue MET1 (Protein).
 Warning: Residue ASP224 in chain has different type (Protein) from
 starting
 residue MET1 (Protein).
 More than 5 unidentified residues at end of chain - disabling further
 warnings.
 Identified residue LEU219 as a ending terminus.

 My protein has 570 residue, but as you see the gromacs identified
 residue
 LEU219 as a ending terminus.!

 2. when I used -missing option and continued my simulations, after
 energy
 minimization, I extract em.pdb file and I saw the distance between NI
 ion
 in active site with F ion in ligand is much more ( ~5 A) than before in
 complex.pdb. This means my ligand isn't stable in active site and it is
 moving away!

 please help me. what is my mistake?why ligand moving away and why
 gromacs
 doesn't identify end of the protein? Is there a relationship between
 added
 parameters and getting away of ligand?


 You forgot step 5:
>>>
>>>

Re: [gmx-users] add new residue and new atom

2016-01-29 Thread Malihe Hasanzadeh 
Dear Justin,
I know these Force fields as much as I can use them. I use always
AMBER99sb-ILDN in my simulations actually like this time, but I'm sorry for
notify name of force field as incomplete. I copied parameters of Lys
residue from .rtp file in AMBER99sb-ILDN for my new residue (KCX) and only
data of carbamyl group added to it (below) as I said before.
CX   OQ1
CX   OQ2
CXHX
Malihe

On Fri, Jan 29, 2016 at 8:54 PM, Justin Lemkul  wrote:

>
>
> On 1/29/16 12:22 PM, Malihe Hasanzadeh wrote:
>
>> Dear Justin,
>> Is there any way to get parameters of KCX residue for amber99sb-ildn?
>>
>
> Well, how did you get the ones you have?  And are you familiar with what
> the differences are between AMBER99sb and AMBER99sb-ILDN?
>
> -Justin
>
> Thanks
>> Malihe
>>
>> On Fri, Jan 29, 2016 at 8:45 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/29/16 12:13 PM, Malihe Hasanzadeh wrote:
>>>
>>> Dear justin,
 I forgot to write this step here, but I did this step also. I added (KCX
 Protein) in .dat file. But unfortunately as you say the gromacs dosen't
 identify my new residue!


>>> If this were true, pdb2gmx would not tell you otherwise.  You didn't do
>>> what you thought you did, or you modified the wrong files.
>>>
>>> What should I do? Is my added parameters for KCX residue correct?
>>>


>>> Follow the steps exactly in the link I provided.  That's all there is to
>>> it.
>>>
>>> -Justin
>>>
>>> Thanks
>>>
 Malihe

 On Fri, Jan 29, 2016 at 8:26 PM, Justin Lemkul  wrote:



> On 1/29/16 11:52 AM, Malihe Hasanzadeh wrote:
>
> Hi
>
>>
>> I used a PDB structure for MD simulation which it has a carbamylated
>> Lys
>> (KCX 220). This residue via carbamyl group bonded to metal in active
>> site.
>> So I had to define new residue(KCX), I copied parameters of Lys
>> residue
>> and
>> added carbamyl group and added to .rtp file in amber force field
>> (99sb)(gromacs5.0.4). I bring KCX parameters in below:
>>   [ KCX ]
>> [ atoms ]
>> NN   -0.34790 1
>> HH0.27470 2
>>CACT  -0.24000 3
>>HAH1   0.14260 4
>>CBCT  -0.00940 5
>>   HB1HC   0.03620 6
>>   HB2HC   0.03620 7
>>CGCT   0.01870 8
>>   HG1HC   0.01030 9
>>   HG2HC   0.0103010
>>CDCT  -0.0479011
>>   HD1HC   0.0621012
>>   HD2HC   0.0621013
>>CECT  -0.0143014
>>   HE1HP   0.1135015
>>   HE2HP   0.1135016
>>NZN3  -0.3854017
>>   HZ1H0.3400018
>>   HZ2H0.3400019
>>   HZ3H0.3400020
>> CC0.7341021
>> OO   -0.5894022
>>CXC0.7341023
>>HXH0.2747024
>>   OQ1O   -0.5894025
>>   OQ2O   -0.5894026
>> [ bonds ]
>> N H
>> NCA
>>CAHA
>>CACB
>>CA C
>>CB   HB1
>>CB   HB2
>>CBCG
>>CG   HG1
>>CG   HG2
>>CGCD
>>CD   HD1
>>CD   HD2
>>CDCE
>>CE   HE1
>>CE   HE2
>>CENZ
>>NZ   HZ1
>>NZ   HZ2
>>NZ   HZ3
>>NZCX
>> C O
>>-C N
>>CX   OQ1
>>CX   OQ2
>>CXHX
>> [ impropers ]
>>-CCA N H
>>CA+N C O
>>NZ   OQ1CX   OQ2
>>
>> In addition this protein has two Ni ion, that I added its parameters
>> in
>> .atp .itp and .dat files.
>> Also my ligand has a F ion that when I docked with the protein, it
>> closed
>> to Ni ion in active site (distance 2.9 A). when I start MD simulation
>> I
>> faced with two problems:
>>
>> 1. when I run pdb2gmx gives many warning:
>>
>> Identified residue MET1 as a starting terminus.
>> Warning: Residue KCX220 in chain has different type (Other) from
>> starting
>> residue MET1 (Protein).
>> Warning: Residue ILE221 in chain has different type (Protein) from
>> starting
>> residue MET1 (Protein).
>> Warning: Residue HIS222 in chain has different type (Protein) from
>> starting
>> residue MET1 (Protein).
>> Warning: Residue GLU223 in chain has different type (Protein) from
>> starting

Re: [gmx-users] Fattal error in gmx dos

2016-01-29 Thread Alexander Alexander 
Thank you for your response.

Then please how can I have case.trr and case.tng? I had gen_vel = yes in my
case.mdp but no velocity was stored somewhere, I just had case.cpt.
The same error showed up when I used case.cpt instead of case.trr.


One more question is that what the meaning of the following sentence is
that comes in the gmx dos explanation?
 "In order for this to be meaningful the velocities must be saved in the
trajecotry with sufficiently high frequency such as to cover all
vibrations"?
How should I know that that the frequency is high enough to cover all the
vibration? How to reach this point?

Thanks,

Regards,
Alex

On Sat, Jan 30, 2016 at 12:54 AM, Justin Lemkul  wrote:

>
>
> On 1/29/16 6:48 PM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> After convergence of my MD simulation where I got my case.xtc file but not
>> case.trr directly, I produced the the case.trr file by the "gmx trjconv -f
>> case.xtc -o case.trr" towards my "gmx dos" calculation. (I had "gen_vel =
>> yes" in my case.mdp)
>> Then I got below Fatal error when I invoked the gmx dos command normally
>> as
>> "gmx dos -f case.trr -s case.tpr -vacf case_va.xvg -mvacf case_mv.xvg -dos
>> case_dos.xvg -g dos.log"
>>
>> Program gmx dos, VERSION 5.1-rc1
>> Source code file:
>> /home/alex/gromacs-5.1-rc1/src/gromacs/fft/fft_fftw3.cpp,
>> line: 309
>>
>> Fatal error:
>> Error initializing FFTW3 plan.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> I would be so appreciated if one could explain the potential reason for
>> this error.
>>
>>
> Converting .xtc to .trr does not magically produce velocities (which are
> not saved in an .xtc), so you cannot use the resulting .trr file for
> anything that requires velocities.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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[gmx-users] Fattal error in gmx dos

2016-01-29 Thread Alexander Alexander 
Dear Gromacs user,

After convergence of my MD simulation where I got my case.xtc file but not
case.trr directly, I produced the the case.trr file by the "gmx trjconv -f
case.xtc -o case.trr" towards my "gmx dos" calculation. (I had "gen_vel =
yes" in my case.mdp)
Then I got below Fatal error when I invoked the gmx dos command normally as
"gmx dos -f case.trr -s case.tpr -vacf case_va.xvg -mvacf case_mv.xvg -dos
case_dos.xvg -g dos.log"

Program gmx dos, VERSION 5.1-rc1
Source code file: /home/alex/gromacs-5.1-rc1/src/gromacs/fft/fft_fftw3.cpp,
line: 309

Fatal error:
Error initializing FFTW3 plan.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I would be so appreciated if one could explain the potential reason for
this error.

Cheers,
Alex
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Re: [gmx-users] adding water with genbox

2016-01-29 Thread Mark Abraham 
Hi,

Also you can use pressure coupling to shrink a box to then use as a
solvated box.

Mark

On Fri, 29 Jan 2016 22:55 Justin Lemkul  wrote:

>
>
> On 1/29/16 4:16 PM, Irem Altan wrote:
> > Hi,
> >
> > I am using gromacs 4.6, so I still use genbox to solvate the protein I’m
> simulating. How does genbox adjust the density? I am trying to pack water
> molecules in a tight protein unit cell, and genbox is having problems
> packing enough water molecules for the water density to be ~1g/cm^3. If I
> modify vdwradii.dat to shrink the radii a little bit, does that affect the
> maximum density that the solvent can have? In other words, will genbox add
> as many water molecules as it can if the radii are small enough, or will it
> stop when d=1g/cm^3?
> >
>
> genbox takes the input (presumably equilibrated) solvent configuration and
> tiles
> it through the unit cell while using the van der Waals radii to avoid
> atomic
> clashes.  It doesn't use any density information directly.  The new solvate
> module (5.0 and newer) has a -scale option that can modulate this to an
> extent,
> but keep in mind (1) as soon as you equilibrate, everything changes and (2)
> perhaps more importantly, most water models don't actually give the exact
> density of water, anyway.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] freeze group in NPT ensemble in gromacs 5.x

2016-01-29 Thread Justin Lemkul 



On 1/29/16 8:53 PM, jagannath mondal wrote:

Hi
   Previously, with gromacs 4.5.4, I had not experienced any problem with
freeze group in NPT ensemble . However, in gromacs 5.0, the same simulation
is crashing. Any suggestion regarding what is best setup for freeze group
calculation in NPT ensemble in gromacs 5.x


Freezing is a serious perturbation that can induce spurious forces with NPT. 
This combination has never been recommended.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] adding water with genbox

2016-01-29 Thread Justin Lemkul 



On 1/29/16 4:16 PM, Irem Altan wrote:

Hi,

I am using gromacs 4.6, so I still use genbox to solvate the protein I’m 
simulating. How does genbox adjust the density? I am trying to pack water 
molecules in a tight protein unit cell, and genbox is having problems packing 
enough water molecules for the water density to be ~1g/cm^3. If I modify 
vdwradii.dat to shrink the radii a little bit, does that affect the maximum 
density that the solvent can have? In other words, will genbox add as many 
water molecules as it can if the radii are small enough, or will it stop when 
d=1g/cm^3?



genbox takes the input (presumably equilibrated) solvent configuration and tiles 
it through the unit cell while using the van der Waals radii to avoid atomic 
clashes.  It doesn't use any density information directly.  The new solvate 
module (5.0 and newer) has a -scale option that can modulate this to an extent, 
but keep in mind (1) as soon as you equilibrate, everything changes and (2) 
perhaps more importantly, most water models don't actually give the exact 
density of water, anyway.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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* Please search the archive at 
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Re: [gmx-users] Fattal error in gmx dos

2016-01-29 Thread Justin Lemkul 



On 1/29/16 7:10 PM, Alexander Alexander wrote:

Thank you for your response.

Then please how can I have case.trr and case.tng? I had gen_vel = yes in my
case.mdp but no velocity was stored somewhere, I just had case.cpt.
The same error showed up when I used case.cpt instead of case.trr.



The gen_vel keyword has nothing to do with saving information; it randomizes 
velocities at the outset of the simulation (gen = generate, not save).


You want to look through 
http://manual.gromacs.org/documentation/5.1.1/user-guide/mdp-options.html#output-control




One more question is that what the meaning of the following sentence is
that comes in the gmx dos explanation?
  "In order for this to be meaningful the velocities must be saved in the
trajecotry with sufficiently high frequency such as to cover all
vibrations"?
How should I know that that the frequency is high enough to cover all the
vibration? How to reach this point?



The next sentence reads:

"For flexible systems that would be around a few fs between saving."

-Justin


Thanks,

Regards,
Alex

On Sat, Jan 30, 2016 at 12:54 AM, Justin Lemkul  wrote:




On 1/29/16 6:48 PM, Alexander Alexander wrote:


Dear Gromacs user,

After convergence of my MD simulation where I got my case.xtc file but not
case.trr directly, I produced the the case.trr file by the "gmx trjconv -f
case.xtc -o case.trr" towards my "gmx dos" calculation. (I had "gen_vel =
yes" in my case.mdp)
Then I got below Fatal error when I invoked the gmx dos command normally
as
"gmx dos -f case.trr -s case.tpr -vacf case_va.xvg -mvacf case_mv.xvg -dos
case_dos.xvg -g dos.log"

Program gmx dos, VERSION 5.1-rc1
Source code file:
/home/alex/gromacs-5.1-rc1/src/gromacs/fft/fft_fftw3.cpp,
line: 309

Fatal error:
Error initializing FFTW3 plan.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

I would be so appreciated if one could explain the potential reason for
this error.



Converting .xtc to .trr does not magically produce velocities (which are
not saved in an .xtc), so you cannot use the resulting .trr file for
anything that requires velocities.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] freeze group in NPT ensemble in gromacs 5.x

2016-01-29 Thread jagannath mondal 
Hi
  Previously, with gromacs 4.5.4, I had not experienced any problem with
freeze group in NPT ensemble . However, in gromacs 5.0, the same simulation
is crashing. Any suggestion regarding what is best setup for freeze group
calculation in NPT ensemble in gromacs 5.x
Jagannath
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Re: [gmx-users] Fattal error in gmx dos

2016-01-29 Thread Justin Lemkul 



On 1/29/16 6:48 PM, Alexander Alexander wrote:

Dear Gromacs user,

After convergence of my MD simulation where I got my case.xtc file but not
case.trr directly, I produced the the case.trr file by the "gmx trjconv -f
case.xtc -o case.trr" towards my "gmx dos" calculation. (I had "gen_vel =
yes" in my case.mdp)
Then I got below Fatal error when I invoked the gmx dos command normally as
"gmx dos -f case.trr -s case.tpr -vacf case_va.xvg -mvacf case_mv.xvg -dos
case_dos.xvg -g dos.log"

Program gmx dos, VERSION 5.1-rc1
Source code file: /home/alex/gromacs-5.1-rc1/src/gromacs/fft/fft_fftw3.cpp,
line: 309

Fatal error:
Error initializing FFTW3 plan.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I would be so appreciated if one could explain the potential reason for
this error.



Converting .xtc to .trr does not magically produce velocities (which are not 
saved in an .xtc), so you cannot use the resulting .trr file for anything that 
requires velocities.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] adding water with genbox

2016-01-29 Thread Irem Altan 
Hi,

I am using gromacs 4.6, so I still use genbox to solvate the protein I’m 
simulating. How does genbox adjust the density? I am trying to pack water 
molecules in a tight protein unit cell, and genbox is having problems packing 
enough water molecules for the water density to be ~1g/cm^3. If I modify 
vdwradii.dat to shrink the radii a little bit, does that affect the maximum 
density that the solvent can have? In other words, will genbox add as many 
water molecules as it can if the radii are small enough, or will it stop when 
d=1g/cm^3?

Best,
Irem
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Re: [gmx-users] Heat capacity (C_{v}) for a solid

2016-01-29 Thread David van der Spoel 

On 29/01/16 19:54, Alexander Alexander wrote:

Thank you so much for your response.

Concerning to the "-nmol"; this is also what I though that number of B is
the -nmol as whe have A3B , but do not you think that the number of
molecules depends strongly on how molecules or residuals are defined in the
topology file in [ moleculetype ] section? That is why I brought part of my
topology file above. If I had something like
--
[ moleculetype ]
; Namenrexcl
A3B   1

molecules ]
;mol_name number
 A3B 43904
--
then you are right and the -nmol was (#A3B/4), but ... .

I am still wondering if the the Cv here is molar one as unit of it is
"J/mol K"?

By selecting -nmol 10976 you are defining what the molecule is.


Also, no comment please about strange behavior of the Cv-T?
This is not strange, it just warns you to check whether the simulations 
have converged. If not the cV you measure is in fact the drift in the 
energy. So plot your energy and make sure it is converged.





Best regards,

Alex

On Fri, Jan 29, 2016 at 7:37 PM, David van der Spoel 
wrote:


On 29/01/16 19:00, Alexander Alexander wrote:


Dear Gromacs user,

I am trying to calculate the heat capacity at constant volume (C_{v}) in
different temperature for a solid structure with "A_{3}B" chemical
formula.
To do so, I made a big supercell containing totally "43904" atom by
keeping
the rate (#A = 32928 and #B=10976), below is a part of my topology file.
topol.top:
-
[ moleculetype ]
; Namenrexcl
A   1

[ moleculetype ]
; Namenrexcl
B1

[ molecules ]
;mol_name number
 A32928
 B 10976
-

After convergence of the MD simulation I invoked the below command:

"gmx energy -f case.edr -nmol 43904 -fluct_props -o case.xvg"

My first question:
what exactly I should use as "-nmol" in this specific case as explained
above? If it is (#A) or (#B) or (#A+#B)?


Since your formula is A3B I guess the number of "molecules" is the same as
the number of B particles.



Second question:
I was wondering if the Cv printed out in screen after choosing "Total
Energy"  and "Temperature" in gmx energy is relabel?  At least in this
level as I know the Quantum part has not been included yet.  Or I have to
do the temperature numerical derivation of Total energy myself as
Cv=d(U)/d(T).


This is safer. Do the simulations at two or three temperatures and compute
cV = dU/dT if constant volume or cP = dH/dT if constant pressure.




WARNING: Please verify that your simulations are converged and perform
a block-averaging error analysis (not implemented in g_energy yet)
Heat capacity at constant volume Cv   =200.779 J/mol K.

Third question:
If this is Molar heat capacity, am I right?

The last:
Below are the result of Cv in different temperature for this system:

(Cv  J/mol K) - (Temperature K)
37037.700  10
   200.779  50
 40.497  75
   124.360  100
   321.416  150
   620.247  298

I know these Cv do not include any corrections for quantum yet, but still
I
am puzzled about the strange behavior of  Cv versus temperature, I would
be
so thankful if one could explain it for me.

(Version of Gromacs : is 5.1-rc1)

Sincerely,

Alex




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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