Re: [gmx-users] Zn moves away from protein - ligand complex

[HongTham]

Hi Mark,
Sorry that I don't get you. Can you explain a little bit for me? I just
wonder if Zn really moves out of active site, when I display multi box in
VMD, there shouldn't have another Zn bound in there.
Sincerely,
Hongtham
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Re: [gmx-users] Some simple questions about using -rerun in mdrun for energy between two groups

[Sheng Bi]

> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: Tuesday, April 19, 2016
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Cc: 
> Subject: Re: [gmx-users] Some simple questions about using -rerun in mdrun 
> for energy between two groups
> 
> Hi,
> 
> This just works on the original trajectory if you use energy groups in the
> rerun tpr. Whether the numbers are useful is another matter :-)
> 
> Mark
> 
> On Mon, 18 Apr 2016 18:27 Sheng Bi  wrote:
> 
> > Dear GMX Users
> > I have some questions when using -rerun in mdrun to get some specific
> > energy for my groups. Let me describe my question in this way.
> > I have a system containing some groups which include A and B and others.
> > My goal is to calculate the energy between A and B.
> > So Here is my steps:
> > first, I use gmx trjconv to get trajectory contains only A and B called
> > A_B.xtc.
> > Second, I grompp a new tpr which is also only contain group A and B called
> > A_B.tpr.
> > Third, I use mdrun -rerun A_B.xtc -s A_B.tpr -v -deffnm energy_A_B
> > Last, I use gmx energy -f energy_A_B.edr and choose "Total Energy" to get
> > total energy of A_B system.
> > My question is, by this way, I can get the total energy (name it E_total),
> > but in my opinion this energy is composed of the energy
> >
> > between A and A (name it E_A_A), energy between B and B (name it E_B_B),
> > and energy between A and B (name it E_A_B). I only care
> >
> > about E_A_B. By now, I have to repeat above four steps to get E_A_A, and
> > E_B_B, then use E_total minus E_A_A and E_B_B to get E_A_B.
> >
> > This is a very tedious work.
> > I am not quite familiar with -rerun, Is there any ingenious method to get
> > E_A_B ? I am not quite familiar with -rerun?
> > Thanks
> >
> > Sheng bi
> >
> >
> >
> > --
> > PhD student
> > State Key Laboratory of Coal Combustion,
> > School of Energy and Power Engineering,
> > Huazhong University of Science and Technology (HUST),
> > Room 302 Power Building,
> > 1037 Luoyu Road, Wuhan, Hubei 430074 China
> > Email: chrisheng...@hust.edu.cn
> > Phone: (86)27-87548122
> > http://itp.energy.hust.edu.cn
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Yes, you are right.
Thank you Mark:)
--
PhD student
State Key Laboratory of Coal Combustion,
School of Energy and Power Engineering,
Huazhong University of Science and Technology (HUST),
Room 302 Power Building, 
1037 Luoyu Road, Wuhan, Hubei 430074 China
Email:chrisheng...@hust.edu.cn
Phone: (86)27-87548122 
http://itp.energy.hust.edu.cn

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Re: [gmx-users] Some simple questions about using -rerun in mdrun for energy between two groups

[Sheng Bi]

> -Original Messages-
> From: "Justin Lemkul" 
> Sent Time: Tuesday, April 19, 2016
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Some simple questions about using -rerun in mdrun 
> for energy between two groups
> 
> 
> 
> On 4/18/16 1:19 PM, Sheng Bi wrote:
> > Dear GMX Users
> > I have some questions when using -rerun in mdrun to get some specific 
> > energy for my groups. Let me describe my question in this way.
> > I have a system containing some groups which include A and B and others. My 
> > goal is to calculate the energy between A and B.
> > So Here is my steps:
> > first, I use gmx trjconv to get trajectory contains only A and B called 
> > A_B.xtc.
> > Second, I grompp a new tpr which is also only contain group A and B called 
> > A_B.tpr.
> > Third, I use mdrun -rerun A_B.xtc -s A_B.tpr -v -deffnm energy_A_B
> > Last, I use gmx energy -f energy_A_B.edr and choose "Total Energy" to get 
> > total energy of A_B system.
> > My question is, by this way, I can get the total energy (name it E_total), 
> > but in my opinion this energy is composed of the energy
> >
> > between A and A (name it E_A_A), energy between B and B (name it E_B_B), 
> > and energy between A and B (name it E_A_B). I only care
> >
> > about E_A_B. By now, I have to repeat above four steps to get E_A_A, and 
> > E_B_B, then use E_total minus E_A_A and E_B_B to get E_A_B.
> >
> > This is a very tedious work.
> > I am not quite familiar with -rerun, Is there any ingenious method to get 
> > E_A_B ? I am not quite familiar with -rerun?
> 
> Just set:
> 
> energygrps = A B
> 
> and create a new .tpr, which is used for the rerun.
> 
> -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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Oh，I had forgotten energygrps! How stupid:)
Thank you Justin.

--
PhD student
State Key Laboratory of Coal Combustion,
School of Energy and Power Engineering,
Huazhong University of Science and Technology (HUST),
Room 302 Power Building, 
1037 Luoyu Road, Wuhan, Hubei 430074 China
Email:chrisheng...@hust.edu.cn
Phone: (86)27-87548122 
http://itp.energy.hust.edu.cn

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Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Mark Abraham]

Hi,

Convert the units and absorb the factor of two to the minus six. Compare
with other ions present in both representations of such force fields.

Mark

On Tue, 19 Apr 2016 02:21 Pedro Lacerda  wrote:

> Hi Gromacs users,
>
> We are planning a simulation with a metallic (fe+2) attached on the
> protein. The parameters found in [1] cannot be directly inserted on
> ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> slightly different.
>
> Theoreticaly these Lennard-Jones parameters could be used in any PME based
> force field, but it was derived and tested using the AMBER software and
> potential, so it is our current force field of choice. In
> amber99sb-ildn/ffnonbonded.itp the long range interactions are described in
> terms of epsilon (kJ/mol) and sigma (Rmin; nm).
>
> Eq 1:
>
> Lj = 4e ((R/r)^12 - (R/r)^6)
>
> Eq 4.5:
>
> Lj = e ((R/r)^12 - 2(R/r)^6)
>
> Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> calculations to optimize the software. But this occurs at implementation
> level and probably does not have correspondence with the paper.
>
> My question is how can I adapt these parameters so they can be used in
> Gromacs?
>
> (Sorry about the previous email, now the title is correct)
>
> [1]
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
>
> [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
>
> [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
>
>
> Cheers,
>
> Pedro Lacerda
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Re: [gmx-users] Zn moves away from protein - ligand complex

[Mark Abraham]

Hi,

The operations you are doing are working differently on the different
ranges of values that the various groups take over the course of the
simulation. The only way to get a reliable result in all cases is to
actually say what you want - that these three things belong always
together.

Mark

On Tue, 19 Apr 2016 01:55 HongTham  wrote:

> HI Mark,
> I don't get the reason why this happens to Zn since Protein and ligand are
> fix well with trjconv options.
> Would you please point to me particular reason for it? is it simply because
> of visualization or there is really problem with simulation?
>
> Thank you very much
> Hongtham
>
> On Mon, Apr 18, 2016 at 9:35 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you have a cluster of things that make sense to treat together then
> you
> > must tell the tool that, via using such an index group. We haven't yet
> > worked out to implement "do what I want" :-)
> >
> > Mark
> >
> > On Mon, 18 Apr 2016 13:40 HongTham  wrote:
> >
> > > Hello Gromacs users,
> > > I'm running a Zn bound protein - ligand complex simulation. I solvated
> > > whole system in a dodecahedron box. I also meet the problems with
> > boundary
> > > effects. I try to use the gmx trjconv with option -pbc mol -ur compact
> > > -center to fix the problem. However, it doesn't work. The protein and
> > > ligand was centered to the water box, but not Zn ion.
> > > In some frame, Zn stay in the active site, sometime, it appear out site
> > of
> > > the active site. I use VMD and display the system with many box (not
> only
> > > one unit), and see ZN till stay in the active site, but that is Zn of
> > > neighbor box, not the current box. its Zn ion now is stay in the active
> > > site of another box.
> > > I also tried with many option (cluster, nojump, -fit rot+trans) or
> change
> > > the selection of centering but they all useless. The -pbc nojump seems
> to
> > > be fine , it makes the protein + ligand + Zn stay together, but the
> water
> > > molecules are definitely distracted. It is difficult for me to
> calculate
> > > the water molecules within 0.5 to 10 nm of Zn and ligand.
> > > Anyone has been same situation with me? Would anyone give me a
> suggestion
> > > to fix that problem.
> > > Thank you so much.
> > > Best regards,
> > > Hongtham
> > > --
> > > 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] Zn moves away from protein - ligand complex

[HongTham]

HI Mark,
I don't get the reason why this happens to Zn since Protein and ligand are
fix well with trjconv options.
Would you please point to me particular reason for it? is it simply because
of visualization or there is really problem with simulation?

Thank you very much
Hongtham

On Mon, Apr 18, 2016 at 9:35 PM, Mark Abraham 
wrote:

> Hi,
>
> If you have a cluster of things that make sense to treat together then you
> must tell the tool that, via using such an index group. We haven't yet
> worked out to implement "do what I want" :-)
>
> Mark
>
> On Mon, 18 Apr 2016 13:40 HongTham  wrote:
>
> > Hello Gromacs users,
> > I'm running a Zn bound protein - ligand complex simulation. I solvated
> > whole system in a dodecahedron box. I also meet the problems with
> boundary
> > effects. I try to use the gmx trjconv with option -pbc mol -ur compact
> > -center to fix the problem. However, it doesn't work. The protein and
> > ligand was centered to the water box, but not Zn ion.
> > In some frame, Zn stay in the active site, sometime, it appear out site
> of
> > the active site. I use VMD and display the system with many box (not only
> > one unit), and see ZN till stay in the active site, but that is Zn of
> > neighbor box, not the current box. its Zn ion now is stay in the active
> > site of another box.
> > I also tried with many option (cluster, nojump, -fit rot+trans) or change
> > the selection of centering but they all useless. The -pbc nojump seems to
> > be fine , it makes the protein + ligand + Zn stay together, but the water
> > molecules are definitely distracted. It is difficult for me to calculate
> > the water molecules within 0.5 to 10 nm of Zn and ligand.
> > Anyone has been same situation with me? Would anyone give me a suggestion
> > to fix that problem.
> > Thank you so much.
> > Best regards,
> > Hongtham
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] trjconv index mismatch

[Alex]

You, my friend, are a genius. All worked, thanks tons.

Alex

On Mon, Apr 18, 2016 at 5:40 PM, Justin Lemkul  wrote:

>
>
> On 4/18/16 7:39 PM, Alex wrote:
>
>> The atom groups, as they appear in the coordinate input, are:
>>
>> 1. DNA atoms (labeled DA, DC, etc)
>> 2. CNT atoms
>> 3. SOL
>> 4. Ions
>>
>> I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
>> compressed trajectory, respectively):
>>
>> step 1:
>>   gmx convert-tpr -s prod.tpr -o cnt_only.tpr
>> selected CNT
>> step 2:
>> trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb
>>
>> this last one does not even bother to open the menu, it throws the
>> following:
>>
>> ---
>> Program trjconv, VERSION 5.0.5
>> Source code file:
>> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c,
>> line:
>> 957
>>
>> Software inconsistency error:
>> Position restraint coordinates are missing
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> Any thoughts?
>>
>>
> You need to make:
>
> 1. New .tpr with no restraints
> 2. Subset .tpr with just the CNT
>
>
> -Justin
>
>
>>
>> On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/16 7:27 PM, Alex wrote:
>>>
>>> Yes, there are more atoms in the system, but only 2837 of them are
 labeled
 "CNT.' Well, I could share the files with you, of course, but you're
 running the latest version, aren't you? :)


 As you might expect, yes.
>>>
>>> Do the atom numbers of the CNT start from 1, or is there something else
>>> listed before it in the coordinates and topology?  If that's the case,
>>> making a matching .tpr via convert-tpr is the only option.
>>>
>>> -Justin
>>>
>>>
>>> On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:
>>>



> On 4/18/16 7:20 PM, Alex wrote:
>
> Justin,
>
>>
>> I understand what you're saying, but for the life of me I can't
>> understand
>> where this discrepancy is coming from, because the input coordinates
>> have
>> 2837 CNT atoms, and trjconv selector menu lists that number correctly.
>> Completely lost here. Are there any alternatives to output (in mdp)
>> the
>> correct group?
>>
>>
>> Without access to your files, there's nothing else I can really tell
>>
> you.
> Presumably there are more atoms in the system, yes?  Your index group
> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing
> the
> .tpr properly (use convert-tpr to output a matching .tpr that has only
> CNT
> and try again).  I feel like there was an issue with this some time
> ago;
> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>
> -Justin
>
>
> Alex
>
>
>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul 
>> wrote:
>>
>>
>>
>> On 4/18/16 6:17 PM, Alex wrote:
>>>
>>> Hi all,
>>>
>>>
 I've got a system that includes a group named "CNT" consisting of
 2837
 atoms. To save space, I am outputting (at a very high rate) a
 compressed
 trajectory that contains only that group. The GMX version is 5.0.5.
 Here's
 the relevant mdp excerpt:


 nstxout =  1
 nstcomm =  1000
 nstxout-compressed  =  10
 compressed-x-grps   =  CNT
 nstvout =  1000
 nstfout =  500
 nstlog  =  100
 nstenergy   =  500
 nstlist =  20

 Upon trying to convert the compressed trajectory, after selecting
 the
 appropriate group from the menu (CNT, 2837 atoms), I get:

 command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

 output:
 ---
 Program trjconv, VERSION 5.0.5
 Source code file:


 /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
 line: 1330

 Fatal error:
 Index[2645] 2838 is larger than the number of atoms in the
 trajectory file (2837). There is a mismatch in the contents
 of your -f, -s and/or -n files.
 For more information and tips for troubleshooting, please check the
 GROMACS
 website at http://www.gromacs.org/Documentation/Errors

 Where's this single-atom discrepancy coming from? Any suggestions?


 Whatever you selected as output contains more atoms than are in the

 trajectory.  Note that it's not necessarily a single-atom
>>> 

Re: [gmx-users] trjconv index mismatch

[Justin Lemkul]

On 4/18/16 7:39 PM, Alex wrote:

The atom groups, as they appear in the coordinate input, are:

1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions

I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):

step 1:
  gmx convert-tpr -s prod.tpr -o cnt_only.tpr
selected CNT
step 2:
trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb

this last one does not even bother to open the menu, it throws the
following:

---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line:
957

Software inconsistency error:
Position restraint coordinates are missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Any thoughts?



You need to make:

1. New .tpr with no restraints
2. Subset .tpr with just the CNT

-Justin




On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul  wrote:




On 4/18/16 7:27 PM, Alex wrote:


Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)



As you might expect, yes.

Do the atom numbers of the CNT start from 1, or is there something else
listed before it in the coordinates and topology?  If that's the case,
making a matching .tpr via convert-tpr is the only option.

-Justin


On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:





On 4/18/16 7:20 PM, Alex wrote:

Justin,


I understand what you're saying, but for the life of me I can't
understand
where this discrepancy is coming from, because the input coordinates
have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) the
correct group?


Without access to your files, there's nothing else I can really tell

you.
Presumably there are more atoms in the system, yes?  Your index group
somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
.tpr properly (use convert-tpr to output a matching .tpr that has only
CNT
and try again).  I feel like there was an issue with this some time ago;
5.0.5 is considered old nowadays so the bug should have been fixed :)

-Justin


Alex



On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:




On 4/18/16 6:17 PM, Alex wrote:

Hi all,



I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a
compressed
trajectory that contains only that group. The GMX version is 5.0.5.
Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:

/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?


Whatever you selected as output contains more atoms than are in the


trajectory.  Note that it's not necessarily a single-atom discrepancy,
it's
just that the fatal error is triggered as soon as an index that is out
of
range is identified.  You're only outputting CNT, and presumably the
.tpr
contains more atoms, so the selection you're making can only be CNT or
some
subset of those atoms.

-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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send a mail to 

Re: [gmx-users] trjconv index mismatch

[Alex]

The atom groups, as they appear in the coordinate input, are:

1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions

I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):

step 1:
 gmx convert-tpr -s prod.tpr -o cnt_only.tpr
selected CNT
step 2:
trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb

this last one does not even bother to open the menu, it throws the
following:

---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line:
957

Software inconsistency error:
Position restraint coordinates are missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Any thoughts?



On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul  wrote:

>
>
> On 4/18/16 7:27 PM, Alex wrote:
>
>> Yes, there are more atoms in the system, but only 2837 of them are labeled
>> "CNT.' Well, I could share the files with you, of course, but you're
>> running the latest version, aren't you? :)
>>
>>
> As you might expect, yes.
>
> Do the atom numbers of the CNT start from 1, or is there something else
> listed before it in the coordinates and topology?  If that's the case,
> making a matching .tpr via convert-tpr is the only option.
>
> -Justin
>
>
> On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/16 7:20 PM, Alex wrote:
>>>
>>> Justin,

 I understand what you're saying, but for the life of me I can't
 understand
 where this discrepancy is coming from, because the input coordinates
 have
 2837 CNT atoms, and trjconv selector menu lists that number correctly.
 Completely lost here. Are there any alternatives to output (in mdp) the
 correct group?


 Without access to your files, there's nothing else I can really tell
>>> you.
>>> Presumably there are more atoms in the system, yes?  Your index group
>>> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
>>> .tpr properly (use convert-tpr to output a matching .tpr that has only
>>> CNT
>>> and try again).  I feel like there was an issue with this some time ago;
>>> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>>>
>>> -Justin
>>>
>>>
>>> Alex
>>>

 On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:



> On 4/18/16 6:17 PM, Alex wrote:
>
> Hi all,
>
>>
>> I've got a system that includes a group named "CNT" consisting of 2837
>> atoms. To save space, I am outputting (at a very high rate) a
>> compressed
>> trajectory that contains only that group. The GMX version is 5.0.5.
>> Here's
>> the relevant mdp excerpt:
>>
>>
>> nstxout =  1
>> nstcomm =  1000
>> nstxout-compressed  =  10
>> compressed-x-grps   =  CNT
>> nstvout =  1000
>> nstfout =  500
>> nstlog  =  100
>> nstenergy   =  500
>> nstlist =  20
>>
>> Upon trying to convert the compressed trajectory, after selecting the
>> appropriate group from the menu (CNT, 2837 atoms), I get:
>>
>> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>>
>> output:
>> ---
>> Program trjconv, VERSION 5.0.5
>> Source code file:
>>
>> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
>> line: 1330
>>
>> Fatal error:
>> Index[2645] 2838 is larger than the number of atoms in the
>> trajectory file (2837). There is a mismatch in the contents
>> of your -f, -s and/or -n files.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> Where's this single-atom discrepancy coming from? Any suggestions?
>>
>>
>> Whatever you selected as output contains more atoms than are in the
>>
> trajectory.  Note that it's not necessarily a single-atom discrepancy,
> it's
> just that the fatal error is triggered as soon as an index that is out
> of
> range is identified.  You're only outputting CNT, and presumably the
> .tpr
> contains more atoms, so the selection you're making can only be CNT or
> some
> subset of those atoms.
>
> -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.
> 

Re: [gmx-users] trjconv index mismatch

[Justin Lemkul]

On 4/18/16 7:27 PM, Alex wrote:

Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)



As you might expect, yes.

Do the atom numbers of the CNT start from 1, or is there something else listed 
before it in the coordinates and topology?  If that's the case, making a 
matching .tpr via convert-tpr is the only option.


-Justin


On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:




On 4/18/16 7:20 PM, Alex wrote:


Justin,

I understand what you're saying, but for the life of me I can't understand
where this discrepancy is coming from, because the input coordinates have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) the
correct group?



Without access to your files, there's nothing else I can really tell you.
Presumably there are more atoms in the system, yes?  Your index group
somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
.tpr properly (use convert-tpr to output a matching .tpr that has only CNT
and try again).  I feel like there was an issue with this some time ago;
5.0.5 is considered old nowadays so the bug should have been fixed :)

-Justin


Alex


On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:




On 4/18/16 6:17 PM, Alex wrote:

Hi all,


I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5.
Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?


Whatever you selected as output contains more atoms than are in the

trajectory.  Note that it's not necessarily a single-atom discrepancy,
it's
just that the fatal error is triggered as soon as an index that is out of
range is identified.  You're only outputting CNT, and presumably the .tpr
contains more atoms, so the selection you're making can only be CNT or
some
subset of those atoms.

-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
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* For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.



--
==

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
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* For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.



--
==

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

Re: [gmx-users] trjconv index mismatch

[Alex]

Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)

On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul  wrote:

>
>
> On 4/18/16 7:20 PM, Alex wrote:
>
>> Justin,
>>
>> I understand what you're saying, but for the life of me I can't understand
>> where this discrepancy is coming from, because the input coordinates have
>> 2837 CNT atoms, and trjconv selector menu lists that number correctly.
>> Completely lost here. Are there any alternatives to output (in mdp) the
>> correct group?
>>
>>
> Without access to your files, there's nothing else I can really tell you.
> Presumably there are more atoms in the system, yes?  Your index group
> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
> .tpr properly (use convert-tpr to output a matching .tpr that has only CNT
> and try again).  I feel like there was an issue with this some time ago;
> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>
> -Justin
>
>
> Alex
>>
>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/18/16 6:17 PM, Alex wrote:
>>>
>>> Hi all,

 I've got a system that includes a group named "CNT" consisting of 2837
 atoms. To save space, I am outputting (at a very high rate) a compressed
 trajectory that contains only that group. The GMX version is 5.0.5.
 Here's
 the relevant mdp excerpt:


 nstxout =  1
 nstcomm =  1000
 nstxout-compressed  =  10
 compressed-x-grps   =  CNT
 nstvout =  1000
 nstfout =  500
 nstlog  =  100
 nstenergy   =  500
 nstlist =  20

 Upon trying to convert the compressed trajectory, after selecting the
 appropriate group from the menu (CNT, 2837 atoms), I get:

 command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

 output:
 ---
 Program trjconv, VERSION 5.0.5
 Source code file:
 /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
 line: 1330

 Fatal error:
 Index[2645] 2838 is larger than the number of atoms in the
 trajectory file (2837). There is a mismatch in the contents
 of your -f, -s and/or -n files.
 For more information and tips for troubleshooting, please check the
 GROMACS
 website at http://www.gromacs.org/Documentation/Errors

 Where's this single-atom discrepancy coming from? Any suggestions?


 Whatever you selected as output contains more atoms than are in the
>>> trajectory.  Note that it's not necessarily a single-atom discrepancy,
>>> it's
>>> just that the fatal error is triggered as soon as an index that is out of
>>> range is identified.  You're only outputting CNT, and presumably the .tpr
>>> contains more atoms, so the selection you're making can only be CNT or
>>> some
>>> subset of those atoms.
>>>
>>> -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
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> 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
> 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 

Re: [gmx-users] trjconv index mismatch

[Justin Lemkul]

On 4/18/16 7:20 PM, Alex wrote:

Justin,

I understand what you're saying, but for the life of me I can't understand
where this discrepancy is coming from, because the input coordinates have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) the
correct group?



Without access to your files, there's nothing else I can really tell you. 
Presumably there are more atoms in the system, yes?  Your index group somehow 
specifies out-of-range atoms.  Or maybe trjconv isn't parsing the .tpr properly 
(use convert-tpr to output a matching .tpr that has only CNT and try again).  I 
feel like there was an issue with this some time ago; 5.0.5 is considered old 
nowadays so the bug should have been fixed :)


-Justin


Alex

On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul  wrote:




On 4/18/16 6:17 PM, Alex wrote:


Hi all,

I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?



Whatever you selected as output contains more atoms than are in the
trajectory.  Note that it's not necessarily a single-atom discrepancy, it's
just that the fatal error is triggered as soon as an index that is out of
range is identified.  You're only outputting CNT, and presumably the .tpr
contains more atoms, so the selection you're making can only be CNT or some
subset of those atoms.

-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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send a mail to gmx-users-requ...@gromacs.org.



--
==

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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] trjconv index mismatch

[Justin Lemkul]

On 4/18/16 6:17 PM, Alex wrote:

Hi all,

I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?



Whatever you selected as output contains more atoms than are in the trajectory. 
 Note that it's not necessarily a single-atom discrepancy, it's just that the 
fatal error is triggered as soon as an index that is out of range is identified. 
 You're only outputting CNT, and presumably the .tpr contains more atoms, so 
the selection you're making can only be CNT or some subset of those atoms.


-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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] trjconv index mismatch

[Juan Manuel Aceves-Hernandez]

Dear all, is there an international workshop about Gromacs in America or
Europe the near future?.


2016-04-18 17:17 GMT-05:00 Alex :

> Hi all,
>
> I've got a system that includes a group named "CNT" consisting of 2837
> atoms. To save space, I am outputting (at a very high rate) a compressed
> trajectory that contains only that group. The GMX version is 5.0.5. Here's
> the relevant mdp excerpt:
>
>
> nstxout =  1
> nstcomm =  1000
> nstxout-compressed  =  10
> compressed-x-grps   =  CNT
> nstvout =  1000
> nstfout =  500
> nstlog  =  100
> nstenergy   =  500
> nstlist =  20
>
> Upon trying to convert the compressed trajectory, after selecting the
> appropriate group from the menu (CNT, 2837 atoms), I get:
>
> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>
> output:
> ---
> Program trjconv, VERSION 5.0.5
> Source code file:
> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
> line: 1330
>
> Fatal error:
> Index[2645] 2838 is larger than the number of atoms in the
> trajectory file (2837). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Where's this single-atom discrepancy coming from? Any suggestions?
>
> Thanks,
>
> Alex
> --
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-- 
Juan Manuel Aceves Hernández
Laboratorio de Nanomateriales
Tel. 52 55 5623 1999 ext 39431
Tel y Fax 5623 20 68
Unidad de Investigación Multidisciplinaria
Campo 4, Facultad de Estudios Superiores Cuautitlan
Universidad Nacional Autonoma de México
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[gmx-users] trjconv index mismatch

[Alex]

Hi all,

I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:


nstxout =  1
nstcomm =  1000
nstxout-compressed  =  10
compressed-x-grps   =  CNT
nstvout =  1000
nstfout =  500
nstlog  =  100
nstenergy   =  500
nstlist =  20

Upon trying to convert the compressed trajectory, after selecting the
appropriate group from the menu (CNT, 2837 atoms), I get:

command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb

output:
---
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
line: 1330

Fatal error:
Index[2645] 2838 is larger than the number of atoms in the
trajectory file (2837). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Where's this single-atom discrepancy coming from? Any suggestions?

Thanks,

Alex
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Re: [gmx-users] Details of 5.0 benchmark report?

[Szilárd Páll]

On Mon, Apr 18, 2016 at 9:25 PM, Adam Huffman  wrote:
> Hi Szilárd,
>
> Yes, it's certainly not worth a large effort to try and recover the 
> information.
>
> Thanks for the link, which should be very useful.
>
> The next time you're looking at something like this, it might be worth
> trying to capture what might be useful for others to run tests
> themselves.

Certainly, more information could be useful, but let me emphasize:
simple raw details of benchmark setups will be useful for reference
(especially for the experienced), but less useful than a thorough
study/analysis that explains the how and why as well.

Feel free to ask if you'll have further general questions or even
specific ones regarding your machine or simulation systems.

Cheers,
--
Szilárd


>
> Thanks again,
> Adam
>
>
> On Tue, Apr 12, 2016 at 5:36 PM, Szilárd Páll  wrote:
>> Adam,
>>
>> The job scripts used in those benchmarks are all specific to the
>> machines, and while admittedly the launch configuration information
>> could be useful to have next to each data point, I'm afraid we don't
>> have such data readily extracted from the run logs, I believe. I did
>> not compile the document myself, but unless such data has been parsed
>> and it's just not presented, it would be a quite large effort to go
>> back and extract such information for quite little benefit (as the
>> exact ranks/thread configurations will change with GROMACS versions,
>> compilers, libraries, machine load, etc.)
>>
>> I recommend you to have a look at recent benchmark papers that contain
>> detailed information on what to tune and how to run parallel jobs,
>> e.g.
>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full
>> Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Mon, Apr 11, 2016 at 2:00 PM, Adam Huffman  wrote:
>>> Hello
>>>
>>> Ideal would be to have the command-lines that were used, for those of
>>> us that aren't GROMACS experts.
>>>
>>> Cheers,
>>> Adam
>>>
>>> On Tue, Mar 8, 2016 at 5:08 PM, Szilárd Páll  wrote:
 Hi,

 What details are you interested in? IIRC the inputs are clearly specified
 (although perhaps not provided there).

 --
 Szilárd

 On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman  
 wrote:

> Hello
>
> Are details of the running of the benchmarks reported for version 5.0
> available anywhere?
>
> I'm referring to the report published at:
>
> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf
>
> I would like to be able to run these myself, on three different systems.
>
>
> Cheers,
> Adam
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Re: [gmx-users] Details of 5.0 benchmark report?

[Adam Huffman]

Hi Szilárd,

Yes, it's certainly not worth a large effort to try and recover the information.

Thanks for the link, which should be very useful.

The next time you're looking at something like this, it might be worth
trying to capture what might be useful for others to run tests
themselves.

Thanks again,
Adam


On Tue, Apr 12, 2016 at 5:36 PM, Szilárd Páll  wrote:
> Adam,
>
> The job scripts used in those benchmarks are all specific to the
> machines, and while admittedly the launch configuration information
> could be useful to have next to each data point, I'm afraid we don't
> have such data readily extracted from the run logs, I believe. I did
> not compile the document myself, but unless such data has been parsed
> and it's just not presented, it would be a quite large effort to go
> back and extract such information for quite little benefit (as the
> exact ranks/thread configurations will change with GROMACS versions,
> compilers, libraries, machine load, etc.)
>
> I recommend you to have a look at recent benchmark papers that contain
> detailed information on what to tune and how to run parallel jobs,
> e.g.
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full
> Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Apr 11, 2016 at 2:00 PM, Adam Huffman  wrote:
>> Hello
>>
>> Ideal would be to have the command-lines that were used, for those of
>> us that aren't GROMACS experts.
>>
>> Cheers,
>> Adam
>>
>> On Tue, Mar 8, 2016 at 5:08 PM, Szilárd Páll  wrote:
>>> Hi,
>>>
>>> What details are you interested in? IIRC the inputs are clearly specified
>>> (although perhaps not provided there).
>>>
>>> --
>>> Szilárd
>>>
>>> On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman  wrote:
>>>
 Hello

 Are details of the running of the benchmarks reported for version 5.0
 available anywhere?

 I'm referring to the report published at:

 http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf

 I would like to be able to run these myself, on three different systems.


 Cheers,
 Adam
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 send a mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Dihedral convention

[Christopher Neale]

Dear Mark:

I don't mean to carry this thread beyond its natural life, but I think the OP 
is referring to improper dihedrals, harmonic type and not to improper 
dihedrals, periodic type (or maybe I just don't get how "cos(n * phi + phi_0)" 
is related to the harmonic type?)

Regarding an improper harmonic type defined in eq. 4.5.9 in section 4.2.12, the 
manual text only seems like a complete definition if:
(1) there is no such thing as zeta<0 -- this actually makes sense to me, but I 
think I was thrown off by the x-axis of Fig. 4.9, whose label should probably 
be "zeta_ijkl - zeta_0" (as opposed to simply reading as "zeta"). Just to 
clarify, this Fig. 4.9 is referred to in the text above as relating to the 
improper harmonic type.
(2) it's obvious how to distinguish between zeta=60 and zeta=120 -- this I 
don't understand. Both angles exist so how do you decide which one to choose?
(3) Whether or not zeta values of 20, -20, 340, and 380 are all considered to 
represent the same state -- this seems to me like it has a component of 
programming choice in it, so it might be useful to define that choice, although 
one that I admit is easy to test.

Thank you,
Chris.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: 18 April 2016 06:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Dihedral convention

Hi,
On Thu, 14 Apr 2016 21:10 Christopher Neale 
wrote:

> Where? I took a look at v5.1.2 manual section 4.2.12 and could not find
> it, hence my suggestion to test it out. I note that there is indeed some
> definition in section 4.2.13: "Proper dihedral angles are defined according
> to the IUPAC/IUB convention, where φ is the angle
> between the ijk and the jkl planes, with zero corresponding to the cis
> configuration (i and l onthe same side)." -- but that specifies that it
> relates to propers


Impropers are defined in the previous section, which refers to the one you
quote, where phi is defined clearly.


> and also it doesn't exactly answer the OP's question about ranges from
> 0-360 or -180 to +180.


This doesn't matter at all. cos(n * phi + phi_0) is invariant under any
increment to phi or phi_0 by an increment of a multiple of a full rotation,
because n is an integer.


> Everything is also complicated by the RB definition "where ψ = φ − 180◦",
> so now it is clear that an "angle" does not always have the same definition.
>

That's life. RB has its roots in the polymer simulation community, who use
a different convention from biomolecular folks. I'm open to ways to improve
the wording, though.

Mark


> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 14 April 2016 14:44
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Dihedral convention
>
> Hi,
>
> Also, the details of angle conventions are all covered in the reference
> manual.
>
> Mark
>
> On Thu, 14 Apr 2016 20:37 Christopher Neale 
> wrote:
>
> > Make a box with a single molecule of n-butane, no pressure coupling or
> > pme, use the sd integrator, test it out?
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Parvez
> Mh
> > 
> > Sent: 14 April 2016 12:47
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Dihedral convention
> >
> > Dr. Lemkul,
> >
> > I understand what you said. My question is, in function type 2 ,there are
> > two parameters 1) force constant and 2) angle of plane. For angle
> > measurement, which convention does gromacs follow, -180 t0 180 or 0 to
> 360?
> >
> > --Masrul
> >
> > On Wed, Apr 13, 2016 at 8:35 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 4/13/16 8:29 PM, Parvez Mh wrote:
> > >
> > >> I am talking about improper dihedral function type 2.
> > >>
> > >>
> > > Impropers are intended to keep planar groups planar, not to restrict
> > other
> > > geometries.  You would be better off with a normal dihedral restraint
> or
> > > potentially figuring out why your force field isn't preserving the
> > desired
> > > geometry.
> > >
> > > -Justin
> > >
> > >
> > > --Masrul
> > >>
> > >> On Wed, Apr 13, 2016 at 7:21 PM, Justin Lemkul 
> wrote:
> > >>
> > >>
> > >>>
> > >>> On 4/13/16 2:51 PM, Parvez Mh wrote:
> > >>>
> > >>> Dear all:
> > 
> >  I would like to  use a harmonic type potential for dihedral. Should
> i
> >  use
> >  angle value (-180 to 180 ) or (0 to 360) convention. My equilibrium
> >  angle
> >  is -64 degree. then what would be the angle -64 or (-64+360=)296
> > degree?
> > 
> > 
> >  

Re: [gmx-users] Get rid of verbosity in Gromacs output

[Justin Lemkul]

On 4/18/16 1:36 PM, Xingcheng Lin wrote:

Hi,

Is there anyway in gromacs5.0 to get rid of the Verbosity output such as
"GROMACS is written by:..." when executing each Gromacs command?



Use -nocopyright -quiet.

-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] Get rid of verbosity in Gromacs output

[Xingcheng Lin]

Hi,

Is there anyway in gromacs5.0 to get rid of the Verbosity output such as
"GROMACS is written by:..." when executing each Gromacs command?

Thank you,
-- 
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Re: [gmx-users] Some simple questions about using -rerun in mdrun for energy between two groups

[Justin Lemkul]

On 4/18/16 1:19 PM, Sheng Bi wrote:

Dear GMX Users
I have some questions when using -rerun in mdrun to get some specific energy 
for my groups. Let me describe my question in this way.
I have a system containing some groups which include A and B and others. My 
goal is to calculate the energy between A and B.
So Here is my steps:
first, I use gmx trjconv to get trajectory contains only A and B called A_B.xtc.
Second, I grompp a new tpr which is also only contain group A and B called 
A_B.tpr.
Third, I use mdrun -rerun A_B.xtc -s A_B.tpr -v -deffnm energy_A_B
Last, I use gmx energy -f energy_A_B.edr and choose "Total Energy" to get total 
energy of A_B system.
My question is, by this way, I can get the total energy (name it E_total), but 
in my opinion this energy is composed of the energy

between A and A (name it E_A_A), energy between B and B (name it E_B_B), and 
energy between A and B (name it E_A_B). I only care

about E_A_B. By now, I have to repeat above four steps to get E_A_A, and E_B_B, 
then use E_total minus E_A_A and E_B_B to get E_A_B.

This is a very tedious work.
I am not quite familiar with -rerun, Is there any ingenious method to get E_A_B 
? I am not quite familiar with -rerun?


Just set:

energygrps = A B

and create a new .tpr, which is used for the rerun.

-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] Some simple questions about using -rerun in mdrun for energy between two groups

[Mark Abraham]

Hi,

This just works on the original trajectory if you use energy groups in the
rerun tpr. Whether the numbers are useful is another matter :-)

Mark

On Mon, 18 Apr 2016 18:27 Sheng Bi  wrote:

> Dear GMX Users
> I have some questions when using -rerun in mdrun to get some specific
> energy for my groups. Let me describe my question in this way.
> I have a system containing some groups which include A and B and others.
> My goal is to calculate the energy between A and B.
> So Here is my steps:
> first, I use gmx trjconv to get trajectory contains only A and B called
> A_B.xtc.
> Second, I grompp a new tpr which is also only contain group A and B called
> A_B.tpr.
> Third, I use mdrun -rerun A_B.xtc -s A_B.tpr -v -deffnm energy_A_B
> Last, I use gmx energy -f energy_A_B.edr and choose "Total Energy" to get
> total energy of A_B system.
> My question is, by this way, I can get the total energy (name it E_total),
> but in my opinion this energy is composed of the energy
>
> between A and A (name it E_A_A), energy between B and B (name it E_B_B),
> and energy between A and B (name it E_A_B). I only care
>
> about E_A_B. By now, I have to repeat above four steps to get E_A_A, and
> E_B_B, then use E_total minus E_A_A and E_B_B to get E_A_B.
>
> This is a very tedious work.
> I am not quite familiar with -rerun, Is there any ingenious method to get
> E_A_B ? I am not quite familiar with -rerun?
> Thanks
>
> Sheng bi
>
>
>
> --
> PhD student
> State Key Laboratory of Coal Combustion,
> School of Energy and Power Engineering,
> Huazhong University of Science and Technology (HUST),
> Room 302 Power Building,
> 1037 Luoyu Road, Wuhan, Hubei 430074 China
> Email: chrisheng...@hust.edu.cn
> Phone: (86)27-87548122
> http://itp.energy.hust.edu.cn
> --
> Gromacs Users mailing list
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Re: [gmx-users] Molecule not minimized and NVT failure

[suniba]

Thank you Justin, I understand the problems with PRODRG. I am switching to ATB 
now but earlier, I performed similar study with different ligand using PRODRG, 
and corrected charges according to the mentioned paper. No problem occured at 
all. I understand all systems are different. I was surprised as the ligand is a 
very simple molecule. Anyhow, now I will rerun using ATB and will contact if 
the problem persists. 
Thank you
Suniba

Sent from my iPhone

> On 18-Apr-2016, at 9:36 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 4/18/16 12:02 PM, suniba wrote:
>> 
>> Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
>> Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I
> 
> After doing my tutorial, you should *not* be using PRODRG for topologies, for 
> the reasons mentioned in that very tutorial.
> 
>> have drawn ligand using chemdraw and minimized the structure using chem3D.
>> However, during energy minimization step in gromacs, the values converge
>> earlier after 490 steps of minimization. This means that structure is not
>> energy minimized properly. Also, during NVT, it crashes very early giving a
> 
> The number of steps has nothing to do with whether or not EM was effective.
> 
>> LINCS warning which is posted frequently in mailing list and the 'water'
>> molecule not settled error. I have gone through all the solutions and
>> according to my knowledge, the problem is with minimization. I am confused
>> now how to minimize the structure properly to avoid the error. The long bond
>> warning might also arise due to bad minimization? Any suggestions please. If
>> require I can paste the ligand co-ordinates.
> 
> Ligand coordinates will tell us nothing of use.  The topology is more 
> instructive, but in general go through: 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> 
> If your topology is straight from PRODRG, that's suspect #1 on my list.
> 
> -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 
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[gmx-users] Some simple questions about using -rerun in mdrun for energy between two groups

[Sheng Bi]

Dear GMX Users
I have some questions when using -rerun in mdrun to get some specific energy 
for my groups. Let me describe my question in this way.
I have a system containing some groups which include A and B and others. My 
goal is to calculate the energy between A and B. 
So Here is my steps:
first, I use gmx trjconv to get trajectory contains only A and B called A_B.xtc.
Second, I grompp a new tpr which is also only contain group A and B called 
A_B.tpr.
Third, I use mdrun -rerun A_B.xtc -s A_B.tpr -v -deffnm energy_A_B
Last, I use gmx energy -f energy_A_B.edr and choose "Total Energy" to get total 
energy of A_B system.
My question is, by this way, I can get the total energy (name it E_total), but 
in my opinion this energy is composed of the energy 

between A and A (name it E_A_A), energy between B and B (name it E_B_B), and 
energy between A and B (name it E_A_B). I only care 

about E_A_B. By now, I have to repeat above four steps to get E_A_A, and E_B_B, 
then use E_total minus E_A_A and E_B_B to get E_A_B. 

This is a very tedious work.
I am not quite familiar with -rerun, Is there any ingenious method to get E_A_B 
? I am not quite familiar with -rerun?
Thanks

Sheng bi

 

--
PhD student
State Key Laboratory of Coal Combustion,
School of Energy and Power Engineering,
Huazhong University of Science and Technology (HUST),
Room 302 Power Building, 
1037 Luoyu Road, Wuhan, Hubei 430074 China
Email: chrisheng...@hust.edu.cn
Phone: (86)27-87548122 
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Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Mark Abraham]

Hi,

I would further speculate that these differences are not even significant.
You can also try rotating the whole system with gmx editconf before you
generate the EM input, and that will be enough to change the order of  the
floating point arithmetic, so that a different final energy minimum will be
found. I don't know offhand what range of energy values you might expect,
but you already have some related data for that, from your multiple EM runs
from different starting points.

I'm also sceptical about whether anything useful can be observed; the
potential energy surface is only somewhat relevant to the properties of the
thermalized ensemble.

Mark

On Mon, 18 Apr 2016 18:12 Justin Lemkul  wrote:

>
>
> On 4/18/16 10:30 AM, Rakesh Sharan wrote:
> > Thanks very much Justin.
> >
> > Actually I am minimization a series of configurations from an
> equilibrated
> > trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I
> need
>
> So, to be clear, you altered the TIP4P topology to use a system of 3
> constraints
> that were held rigid by LINCS, using "constraints = all-bonds" when doing
> the
> simulation?  Simply setting LINCS as the constraint method in the .mdp
> file is
> insufficient to turn off SETTLE (which is always used unless you tell
> mdrun not to).
>
> > the final energy of the energy minimized structures, however, you can see
> > that depending on the choice of constrained algorithm, for few
> > configurations, the final energy is different (e. g. for the attached
> plot
> > -29146 and -29288 kj/mol). Actually, both are following same minimization
>
> The list doesn't allow attachments.
>
> Re-minimizing a configuration with different algorithms may lead to some
> differences, I would suspect.  But the internal geometry should be the
> same, so
> all that's varying will be LJ and electrostatic terms.  You can check by
> doing a
> further decomposition into which term is changing the most.
>
> > trajectory, however, one is finishing before other. This is bit troubling
> > as depending on the choice of constraint algorithm average final energy
> is
> > different even though initial starting configuration is exactly same. I
> > rechecked topology files and they look same apart from constraint
> > specifications.
> >
>
> So let me clarify, because I'm not sure if I follow what you're saying
> (because
> here it sounds like you're talking about running different simulations,
> whereas
> above it sounds like a very different case).  Which is true:
>
> 1. You are doing two simulations from the same starting configuration and
> are
> trying to compare the final energy.
> 2. You are re-minimizing each frame of an existing trajectory and comparing
> energies.
>
> #1 really doesn't make sense, as all MD simulations are chaotic, and I'm
> not
> sure what #2 would achieve.
>
> > I would very much appreciate your view over the plausible origin of this
> > discrepancy. Also, I am wondering whether in both the cases one is doing
> > truly constrained minimization.
> >
>
> If there are no bond or angle energy values, the waters were constrained.
>
> -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] Molecule not minimized and NVT failure

[suniba]

Hi Mark
I corrected the PRODRG charges according to the paper cited in tutorial. The 
final energy after EM was -5.6. Anyhow, I will visualize em results and then 
see what happens. 
Thank you

Sent from my iPhone

> On 18-Apr-2016, at 9:37 pm, Mark Abraham  wrote:
> 
> Hi,
> 
> The number of EM steps doesn't mean anything. The final energy can suggest
> that something sensible happened, but the values depend on what your system
> has in it. You also should visualize the result of the EM and see if that
> fits with your chemical knowledge. PRODRG charges often won't produce
> sensible results.
> 
> Mark
> 
>> On Mon, Apr 18, 2016 at 6:03 PM suniba  wrote:
>> 
>> 
>> Hello users
>> I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore,
>> following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn
>> ligand using chemdraw and minimized the structure using chem3D. However,
>> during energy minimization step in gromacs, the values converge earlier
>> after 490 steps of minimization. This means that structure is not energy
>> minimized properly. Also, during NVT, it crashes very early giving a LINCS
>> warning which is posted frequently in mailing list and the 'water' molecule
>> not settled error. I have gone through all the solutions and according to
>> my knowledge, the problem is with minimization. I am confused now how to
>> minimize the structure properly to avoid the error. The long bond warning
>> might also arise due to bad minimization? Any suggestions please. If
>> require I can paste the ligand co-ordinates.
>> 
>> With Regards
>> Suniba
>> Sent from my iPhone
>> --
>> 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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Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Justin Lemkul]

On 4/18/16 10:30 AM, Rakesh Sharan wrote:

Thanks very much Justin.

Actually I am minimization a series of configurations from an equilibrated
trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I need


So, to be clear, you altered the TIP4P topology to use a system of 3 constraints 
that were held rigid by LINCS, using "constraints = all-bonds" when doing the 
simulation?  Simply setting LINCS as the constraint method in the .mdp file is 
insufficient to turn off SETTLE (which is always used unless you tell mdrun not to).



the final energy of the energy minimized structures, however, you can see
that depending on the choice of constrained algorithm, for few
configurations, the final energy is different (e. g. for the attached plot
-29146 and -29288 kj/mol). Actually, both are following same minimization


The list doesn't allow attachments.

Re-minimizing a configuration with different algorithms may lead to some 
differences, I would suspect.  But the internal geometry should be the same, so 
all that's varying will be LJ and electrostatic terms.  You can check by doing a 
further decomposition into which term is changing the most.



trajectory, however, one is finishing before other. This is bit troubling
as depending on the choice of constraint algorithm average final energy is
different even though initial starting configuration is exactly same. I
rechecked topology files and they look same apart from constraint
specifications.



So let me clarify, because I'm not sure if I follow what you're saying (because 
here it sounds like you're talking about running different simulations, whereas 
above it sounds like a very different case).  Which is true:


1. You are doing two simulations from the same starting configuration and are 
trying to compare the final energy.
2. You are re-minimizing each frame of an existing trajectory and comparing 
energies.


#1 really doesn't make sense, as all MD simulations are chaotic, and I'm not 
sure what #2 would achieve.



I would very much appreciate your view over the plausible origin of this
discrepancy. Also, I am wondering whether in both the cases one is doing
truly constrained minimization.



If there are no bond or angle energy values, the waters were constrained.

-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] Molecule not minimized and NVT failure

[Mark Abraham]

Hi,

The number of EM steps doesn't mean anything. The final energy can suggest
that something sensible happened, but the values depend on what your system
has in it. You also should visualize the result of the EM and see if that
fits with your chemical knowledge. PRODRG charges often won't produce
sensible results.

Mark

On Mon, Apr 18, 2016 at 6:03 PM suniba  wrote:

>
> Hello users
> I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore,
> following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn
> ligand using chemdraw and minimized the structure using chem3D. However,
> during energy minimization step in gromacs, the values converge earlier
> after 490 steps of minimization. This means that structure is not energy
> minimized properly. Also, during NVT, it crashes very early giving a LINCS
> warning which is posted frequently in mailing list and the 'water' molecule
> not settled error. I have gone through all the solutions and according to
> my knowledge, the problem is with minimization. I am confused now how to
> minimize the structure properly to avoid the error. The long bond warning
> might also arise due to bad minimization? Any suggestions please. If
> require I can paste the ligand co-ordinates.
>
> With Regards
> Suniba
> Sent from my iPhone
> --
> 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] Molecule not minimized and NVT failure

[Justin Lemkul]

On 4/18/16 12:02 PM, suniba wrote:


Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I


After doing my tutorial, you should *not* be using PRODRG for topologies, for 
the reasons mentioned in that very tutorial.



have drawn ligand using chemdraw and minimized the structure using chem3D.
However, during energy minimization step in gromacs, the values converge
earlier after 490 steps of minimization. This means that structure is not
energy minimized properly. Also, during NVT, it crashes very early giving a


The number of steps has nothing to do with whether or not EM was effective.


LINCS warning which is posted frequently in mailing list and the 'water'
molecule not settled error. I have gone through all the solutions and
according to my knowledge, the problem is with minimization. I am confused
now how to minimize the structure properly to avoid the error. The long bond
warning might also arise due to bad minimization? Any suggestions please. If
require I can paste the ligand co-ordinates.



Ligand coordinates will tell us nothing of use.  The topology is more 
instructive, but in general go through: 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


If your topology is straight from PRODRG, that's suspect #1 on my list.

-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] doubt about "Ignoring obsolete mdp entry"

[Mark Abraham]

Hi,

If you're trying to use such features, then you want to find out how they
are currently implemented and use those instead. Probably you don't care
about most of them. The defaults are all reasonably sensible, and if there
was some issue that you had to act upon, then you'd get an error or a
warning, rather than a note.

Mark

On Mon, Apr 18, 2016 at 5:34 PM Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi all,
> To calculate delta G of mutation I was following the following tutorial
>
> http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/
>
> However following outputs of grompp is confusing me
>
> Ignoring obsolete mdp entry 'cpp'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Ignoring obsolete mdp entry 'andersen_seed'
> Ignoring obsolete mdp entry 'dihre'
> Ignoring obsolete mdp entry 'dihre-fc'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> Ignoring obsolete mdp entry 'nstcheckpoint'
> Ignoring obsolete mdp entry 'optimize_fft'
> Replacing old mdp entry 'unconstrained_start' by 'continuation'
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
> Replacing old mdp entry 'xtc_precision' by 'compressed-x-precision'
>
> I understand the last 3 line. I will be grateful if someone help me
> understand the first 9 line. There was also notes which I could understand.
>
> NOTE 1 [file md.mdp, line 235]:
>   md.mdp did not specify a value for the .mdp option "cutoff-scheme".
>   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
>   the Verlet scheme was introduced, but the group scheme was still the
>   default. The default is now the Verlet scheme, so you will observe
>   different behaviour.
>
> NOTE 2 [file md.mdp]:
>   Setting nstcalcenergy (100) equal to nstdhdl (50)
>
> NOTE 3 [file md.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
>
>
> Thanks a lot for the help.
>
>
> "A society with free knowledge is better than a society with free food"
>
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
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[gmx-users] Molecule not minimized and NVT failure

[suniba]

Hello users
I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore, 
following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn 
ligand using chemdraw and minimized the structure using chem3D. However, during 
energy minimization step in gromacs, the values converge earlier after 490 
steps of minimization. This means that structure is not energy minimized 
properly. Also, during NVT, it crashes very early giving a LINCS warning which 
is posted frequently in mailing list and the 'water' molecule not settled 
error. I have gone through all the solutions and according to my knowledge, the 
problem is with minimization. I am confused now how to minimize the structure 
properly to avoid the error. The long bond warning might also arise due to bad 
minimization? Any suggestions please. If require I can paste the ligand 
co-ordinates.

With Regards
Suniba
Sent from my iPhone
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[gmx-users] doubt about "Ignoring obsolete mdp entry"

[Tushar Ranjan Moharana]

Hi all,
To calculate delta G of mutation I was following the following tutorial

http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/

However following outputs of grompp is confusing me

Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'domain-decomposition'
Ignoring obsolete mdp entry 'andersen_seed'
Ignoring obsolete mdp entry 'dihre'
Ignoring obsolete mdp entry 'dihre-fc'
Ignoring obsolete mdp entry 'dihre-tau'
Ignoring obsolete mdp entry 'nstdihreout'
Ignoring obsolete mdp entry 'nstcheckpoint'
Ignoring obsolete mdp entry 'optimize_fft'
Replacing old mdp entry 'unconstrained_start' by 'continuation'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc_precision' by 'compressed-x-precision'

I understand the last 3 line. I will be grateful if someone help me
understand the first 9 line. There was also notes which I could understand.

NOTE 1 [file md.mdp, line 235]:
  md.mdp did not specify a value for the .mdp option "cutoff-scheme".
  Probably it was first intended for use with GROMACS before 4.6. In 4.6,
  the Verlet scheme was introduced, but the group scheme was still the
  default. The default is now the Verlet scheme, so you will observe
  different behaviour.

NOTE 2 [file md.mdp]:
  Setting nstcalcenergy (100) equal to nstdhdl (50)

NOTE 3 [file md.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


Thanks a lot for the help.


"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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[gmx-users] potential of mean force of pore formation in the lipid bilayer by using potential of mean constraint force (PMCF) method.

[Mayank Dixit]

Dear All,
I want to calculate the potential of mean force of pore
formation in the lipid bilayer by using potential of mean constraint force
(PMCF) method. Can anybody suggest me how to use pull method to compute the
pmf of pore formation.

How to define the reaction coordinate of pore in the gromacs in the pull
method?

Please response me as soon as possible.

Thanks and Kind regards

-- 


*Mayank  Dixit *
Research Scholar
Department of Chemistry
The city college of New York
Marshak Science Building
160 convent avenue 138th street.
New York, NY-10031
Cell no: 13474767359
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Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Rakesh Sharan]

Thanks very much Justin.

Actually I am minimization a series of configurations from an equilibrated
trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I need
the final energy of the energy minimized structures, however, you can see
that depending on the choice of constrained algorithm, for few
configurations, the final energy is different (e. g. for the attached plot
-29146 and -29288 kj/mol). Actually, both are following same minimization
trajectory, however, one is finishing before other. This is bit troubling
as depending on the choice of constraint algorithm average final energy is
different even though initial starting configuration is exactly same. I
rechecked topology files and they look same apart from constraint
specifications.

I would very much appreciate your view over the plausible origin of this
discrepancy. Also, I am wondering whether in both the cases one is doing
truly constrained minimization.

Best,
Rakesh


Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544 (US).


On Thu, Apr 14, 2016 at 1:07 PM, Rakesh Sharan 
wrote:

> Thanks very much Justin.
>
> Actually I am minimization a series of configurations from an equilibrated
> trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I have
> attached here a minimization trajectory of a configuration using SETTLE and
> LINCS.
>
> I need the final energy of the energy minimized structures, however, you
> can see that depending on the choice of constrained algorithm, for few
> configurations, the final energy is different (e. g. for the attached plot
> -29146 and -29288 kj/mol). This is bit troubling as depending on the choice
> of constraint algorithm average final energy is different even though
> initial starting configuration is exactly same. I rechecked topology files
> and they look same apart from constraint specifications.
>
> I would very much appreciate your view over the plausible origin of this
> discrepancy. Also, I am wondering whether in both the cases one is doing
> truly constrained minimization.
>
> Best,
> Rakesh
>
> 
> Rakesh S. Singh, Ph.D.
> Postdoctoral Research Associate,
> Department of Chemical & Biological Engineering,
> Princeton University,
> Princeton, NJ 08544 (US).
>
>
> On Tue, Apr 12, 2016 at 8:25 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 4/11/16 4:08 PM, Rakesh Sharan wrote:
>>
>>> Hi all,
>>>
>>> I am getting significantly different final energy during energy
>>>
>>
>> How large is the difference?  If it is dramatic, then your coordinates
>> should also be quite different and visualization should provide some
>> clues.  But given that the water molecules are rigid, the only differences
>> will be in nonbonded terms, which means a different configuration.  There's
>> no guarantee that two constraint algorithms will produce identical
>> outcomes, though I would expect them to be close if set up properly.
>>
>> minimization of a box of bulk TIP4P/2005 water using SETTLE and LINCS as
>>> constraint algorithms. I do not know which is more reliable in the sense
>>> that which one is giving correct converged configurations starting from
>>> the
>>> same initial configuration.
>>>
>>> I would highly appreciate your comments/suggestions over this
>>> discrepancy.
>>>
>>> The mdp file that I am using is following:
>>>
>>>
>> The .mdp file is not particularly relevant, as using LINCS vs. SETTLE
>> will have to be done with changes to the topology file.  If you're getting
>> big differences in outcomes, probably whatever modifications you did there
>> are incorrect.
>>
>> -Justin
>>
>>
>> integrator  = steep ; steepest descents energy
>>> minimization
>>> nsteps  = 1  ; maximum number of steps to
>>> integrate
>>>
>>> emtol   = 1.0  ; [kJ/mol/nm] minimization is
>>> converged when max force is < emtol
>>> emstep  = 0.01  ; [nm] initial step-size
>>>
>>> nstxtcout   = 10; [steps] freq to write to
>>> coordinate file
>>> nstlog  = 10; [steps] freq to write energies
>>> to
>>> log file
>>> nstenergy   = 10; [steps] freq to write energies
>>> to
>>> energy file
>>> xtc_grps= System; coordinate group(s) to write to
>>> disk
>>> energygrps  = System; group(s) to write to energy
>>> file
>>>
>>> nstlist = 1 ; [steps] freq to update neighbor
>>> list
>>> ns_type = grid  ; method of updating neighbor
>>> list
>>> pbc = xyz   ; periodic boundary conditions in
>>> all directions
>>> rlist   = 0.95   ; [nm] cut-off distance for the
>>> short-range 

[gmx-users] gmx wham crashes with buffer overflow

[Michail Palaiokostas Avramidis]

Dear gmx users,


I am using gmx wham to analyse umbrella sampling simulations. I have 30 
positions along the reaction coordinate and therefore 30 tpr, pullf and pullx 
files. Each of these files have 100,000 rows, as I save every ps.


When I try to execute wham with the command:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -v -min 0 
-max 29 -zprof0 29


the program is crashing with the Aborted (core dumped) message and a buffer 
overflow error. Can this be due to the large number of samples (100,000) per 
file? Because it crashes even if I add the -b flag to 9.


I would really appreciate any ideas on the topic.

Thank you very much in advance.


Kind Regards,

Michail


PS. The whole message I get, is:

File //npt-res-00.tpr, 1 coordinates, geometry "distance", 
dimensions [N N Y], (1 dimensions)
Pull group coordinates expected in pullx files.
crd 0) k = 1000   position = 0.00115691
*** buffer overflow detected ***: gmx terminated
=== Backtrace: =
/lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7f3c1edba38f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f3c1ee51c9c]
/lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7f3c1ee50b60]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_ffopen+0xfa)[0x7f3c1fc3bf3a]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_fio_open+0x3c3)[0x7f3c1fc5ca13]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_fio_fopen+0xb)[0x7f3c1fc5cdbb]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(read_xvg_legend+0x46)[0x7f3c1fc49ba6]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(_Z12read_pull_xfPKcS0_P16t_UmbrellaHeaderP16t_UmbrellaWindowP17t_UmbrellaOptionsiPfS7_P16t_groupselection+0xbc)[0x7f3c1fe5ffac]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(_Z21read_tpr_pullxf_filesPPcS0_iP16t_UmbrellaHeaderP16t_UmbrellaWindowP17t_UmbrellaOptions+0x131)[0x7f3c1fe616b1]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_wham+0x1018)[0x7f3c1fe677a8]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x1fa)[0x7f3c1fb0641a]
gmx(main+0x84)[0x40be24]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f3c1ed68ec5]
gmx[0x40bf5e]
=== Memory map: 
0040-0043c000 r-xp  08:12 22415410   
/usr/local/gromacs/bin/gmx
0063c000-0063d000 r--p 0003c000 08:12 22415410   
/usr/local/gromacs/bin/gmx
0063d000-0063e000 rw-p 0003d000 08:12 22415410   
/usr/local/gromacs/bin/gmx
0063e000-0063f000 rw-p  00:00 0
00e1e000-00ea5000 rw-p  00:00 0  [heap]
7f3c1c103000-7f3c1c13e000 r-xp  08:12 19923688   
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c13e000-7f3c1c33d000 ---p 0003b000 08:12 19923688   
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c33d000-7f3c1c33e000 r--p 0003a000 08:12 19923688   
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c33e000-7f3c1c33f000 rw-p 0003b000 08:12 19923688   
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c33f000-7f3c1c704000 r-xp  08:12 22413453   
/usr/lib/atlas-base/atlas/libblas.so.3.0
7f3c1c704000-7f3c1c903000 ---p 003c5000 08:12 22413453   
/usr/lib/atlas-base/atlas/libblas.so.3.0
7f3c1c903000-7f3c1c90b000 rw-p 003c4000 08:12 22413453   
/usr/lib/atlas-base/atlas/libblas.so.3.0
7f3c1c90b000-7f3c1ca22000 r-xp  08:12 19925662   
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1ca22000-7f3c1cc22000 ---p 00117000 08:12 19925662   
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1cc22000-7f3c1cc23000 r--p 00117000 08:12 19925662   
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1cc23000-7f3c1cc25000 rw-p 00118000 08:12 19925662   
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1cc25000-7f3c1cfb1000 r-xp  08:12 22413457   
/usr/lib/atlas-base/libatlas.so.3.0
7f3c1cfb1000-7f3c1d1b ---p 0038c000 08:12 22413457   
/usr/lib/atlas-base/libatlas.so.3.0
7f3c1d1b-7f3c1d1b8000 rw-p 0038b000 08:12 22413457   
/usr/lib/atlas-base/libatlas.so.3.0
7f3c1d1b8000-7f3c1d1d9000 r-xp  08:12 22413446   
/usr/lib/atlas-base/libcblas.so.3.0
7f3c1d1d9000-7f3c1d3d8000 ---p 00021000 08:12 22413446   
/usr/lib/atlas-base/libcblas.so.3.0
7f3c1d3d8000-7f3c1d3d9000 rw-p 0002 08:12 22413446   
/usr/lib/atlas-base/libcblas.so.3.0
7f3c1d3d9000-7f3c1d3e6000 r-xp  08:12 19924391   
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f3c1d3e6000-7f3c1d5e6000 ---p d000 08:12 19924391   
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f3c1d5e6000-7f3c1d5e7000 r--p 

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[James Starlight]

Ok thanks I will look into the tutorial!

J.

2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
> @Michael: Yes, you are right, a protein is a protein. IIRC the martinize
> script does the same as pdb2gmx in this case.
> @James: It really sounds like you want to do DAFT.
> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
> seems to contain an tutorial. Otherwise, consider contacting the author of
> the paper (T Wassenaar).
>
> Peter
>
> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
> wrote:
>
>> Hi James,
>>
>> My guess is that running a two (unbound) protein simulation with the
>> MARTINI force-field will be the same as if it was all atom. Build two
>> separate protein topologies (with Martini force-fields) as *.itp files to
>> include in your *.top and go from there. The topology file is what grompp
>> uses to determine bonding, so if the topology file doesn't have the two
>> proteins bound, they won't be. If I remember correctly, you can see an
>> example (all-atom) topology file to work with if you use pdb2gmx for a pdb
>> that contains 2 chains (with the proper flag the chains will be split).
>>
>> -Micholas
>>
>> ===
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
>> Starlight 
>> Sent: Monday, April 18, 2016 9:43 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition
>>
>> It seems like smth very complicated :)
>>
>> I just need to put two different proteins in the system - one in the
>> membrane (A) and one in the water (B) and simulate it independently 10
>> times to collect statistics about associations of A and B during those
>> runs. The problems that I don't know how to put 2 different unbound
>> proteins in the MARTINI system.
>>
>> James
>>
>> 2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
>> > Hi,
>> >
>> > I assume you want to study the binding of your water soluble protein to
>> > your membrane(protein). DAFT was created to do just this. DOI:
>> > 10.1021/ct5010092
>> >
>> > Peter
>> >
>> > On Fri, Apr 15, 2016 at 3:37 PM, James Starlight > >
>> > wrote:
>> >
>> >> Dear Gromacs users!
>> >>
>> >> I am looking for some tutorial for the MARTINI simulation of
>> >> protein-protein recognition dealing with the big membrane protein
>> >> simulated within the membrane and its assosiation with the small water
>> >> soluble protein. The question - is it possible in existing Martini
>> >> system conisdted of only membrane protein solvated in membrane with
>> >> water to
>> >> i) increase box size on Z
>> >> ii)add some water
>> >> iii) put another water soluble protein in new space (on the distance
>> >> of the initial membrane protein complex)
>> >> iv) edit topology of new system and run new md
>> >>
>> >> assuming that i,ii and iv are trivial the problem here is the iii step
>> :-)
>> >>
>> >> or alternatively if I would like to run new simulation with those 2
>> >> proteins (in the unbound form) how I can prepare such complex system
>> >> consisted of big protein in membrane plus water soluble protein
>> >> unbound from it?
>> >>
>> >> Thanks!
>> >>
>> >> Gleb
>> >> --
>> >> 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.
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>> * Please search the archive at
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Re: [gmx-users] wierd gro file output.

[Mark Abraham]

Hi,

What were the actual commands, e.g. to grompp and trjconv that produced
such results? I think you've done something mutually inconsistent.

Mark

On Mon, Apr 18, 2016 at 3:22 PM abhishek khetan  wrote:

> Dear gmx-users,
>
> I was analysing some trajectory files from a box of acetonitrile solvents
> when i realised that despite using trjconv -pbc whole and then trjconv -pbc
> no jump, the molecules appeared to be broken when visualising using pymol.
>
> When i looked that the gro file, the final gro file was of the kind:
>
> ACN216
>  1296
> 1ACN C11   0.030   0.065   2.621
> 2ACN H22   0.110   0.009   2.572
> 3ACN H33  -0.006   0.008   2.706
> 4ACN H44  -0.052   0.080   2.550
> 5ACN C55   0.080   0.195   2.666
> 6ACN N66   0.120   0.298   2.702
> 1ACN C17   1.963   1.695   0.110
> 2ACN H28   2.012   1.649   0.196
> 3ACN H39   1.866   1.647   0.095
> 4ACN H4   10   2.024   1.681   0.021
> 5ACN C5   11   1.944   1.838   0.136
> 6ACN N6   12   1.928   1.951   0.157
> 1ACN C1   13   0.033   2.237   2.583
> 2ACN H2   14   0.129   2.281   2.609
> 3ACN H3   15  -0.009   2.290   2.497
> 4ACN H4   16  -0.035   2.247   2.667
>  
>  
>
> Where as the input file at the beginning of the simulations had the form
>
> GROup of MAchos and Cynical Suckers
>  1296
> 1ACN C11   0.000  -0.117   0.000
> 1ACN H22   0.102  -0.154   0.000
> 1ACN H33  -0.051  -0.154   0.089
> 1ACN H44  -0.051  -0.154  -0.089
> 1ACN C55   0.000   0.028   0.000
> 1ACN N66   0.000   0.143   0.000
> 2ACN C17   2.050   1.716   0.214
> 2ACN H28   2.149   1.683   0.242
> 2ACN H39   1.984   1.707   0.300
> 2ACN H4   10   2.012   1.653   0.134
> 2ACN C5   11   2.054   1.855   0.169
> 2ACN N6   12   2.058   1.964   0.135
> 3ACN C1   13   2.580   2.268   2.635
> 3ACN H2   14   2.667   2.329   2.609
> 3ACN H3   15   2.506   2.278   2.557
> 3ACN H4   16   2.539   2.304   2.729
>
> As you can see the output gro file has teh residue numbeing gobbled up,
> although in a very orderly manner. Could you please suggest whats going on.
> I was hoping that using -pbc whole would not make any difference because
> none of the bond would be broken in my simulations. However, even after
> using -pbc whole in the trjconv routine, I find molecules broken
>
> Thanks for the help in advance.
>
> --
> MfG,
> abhishek
> --
> 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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Re: [gmx-users] MARTINI simulation of protein-protein recognition

[Kroon, P.C.]

@Michael: Yes, you are right, a protein is a protein. IIRC the martinize
script does the same as pdb2gmx in this case.
@James: It really sounds like you want to do DAFT.
http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
seems to contain an tutorial. Otherwise, consider contacting the author of
the paper (T Wassenaar).

Peter

On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
wrote:

> Hi James,
>
> My guess is that running a two (unbound) protein simulation with the
> MARTINI force-field will be the same as if it was all atom. Build two
> separate protein topologies (with Martini force-fields) as *.itp files to
> include in your *.top and go from there. The topology file is what grompp
> uses to determine bonding, so if the topology file doesn't have the two
> proteins bound, they won't be. If I remember correctly, you can see an
> example (all-atom) topology file to work with if you use pdb2gmx for a pdb
> that contains 2 chains (with the proper flag the chains will be split).
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
> Starlight 
> Sent: Monday, April 18, 2016 9:43 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition
>
> It seems like smth very complicated :)
>
> I just need to put two different proteins in the system - one in the
> membrane (A) and one in the water (B) and simulate it independently 10
> times to collect statistics about associations of A and B during those
> runs. The problems that I don't know how to put 2 different unbound
> proteins in the MARTINI system.
>
> James
>
> 2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
> > Hi,
> >
> > I assume you want to study the binding of your water soluble protein to
> > your membrane(protein). DAFT was created to do just this. DOI:
> > 10.1021/ct5010092
> >
> > Peter
> >
> > On Fri, Apr 15, 2016 at 3:37 PM, James Starlight  >
> > wrote:
> >
> >> Dear Gromacs users!
> >>
> >> I am looking for some tutorial for the MARTINI simulation of
> >> protein-protein recognition dealing with the big membrane protein
> >> simulated within the membrane and its assosiation with the small water
> >> soluble protein. The question - is it possible in existing Martini
> >> system conisdted of only membrane protein solvated in membrane with
> >> water to
> >> i) increase box size on Z
> >> ii)add some water
> >> iii) put another water soluble protein in new space (on the distance
> >> of the initial membrane protein complex)
> >> iv) edit topology of new system and run new md
> >>
> >> assuming that i,ii and iv are trivial the problem here is the iii step
> :-)
> >>
> >> or alternatively if I would like to run new simulation with those 2
> >> proteins (in the unbound form) how I can prepare such complex system
> >> consisted of big protein in membrane plus water soluble protein
> >> unbound from it?
> >>
> >> Thanks!
> >>
> >> Gleb
> >> --
> >> Gromacs Users mailing list
> >>
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Re: [gmx-users] MARTINI simulation of protein-protein recognition

[Smith, Micholas D.]

Hi James,

My guess is that running a two (unbound) protein simulation with the MARTINI 
force-field will be the same as if it was all atom. Build two separate protein 
topologies (with Martini force-fields) as *.itp files to include in your *.top 
and go from there. The topology file is what grompp uses to determine bonding, 
so if the topology file doesn't have the two proteins bound, they won't be. If 
I remember correctly, you can see an example (all-atom) topology file to work 
with if you use pdb2gmx for a pdb that contains 2 chains (with the proper flag 
the chains will be split).

-Micholas

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of James 
Starlight 
Sent: Monday, April 18, 2016 9:43 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition

It seems like smth very complicated :)

I just need to put two different proteins in the system - one in the
membrane (A) and one in the water (B) and simulate it independently 10
times to collect statistics about associations of A and B during those
runs. The problems that I don't know how to put 2 different unbound
proteins in the MARTINI system.

James

2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
> Hi,
>
> I assume you want to study the binding of your water soluble protein to
> your membrane(protein). DAFT was created to do just this. DOI:
> 10.1021/ct5010092
>
> Peter
>
> On Fri, Apr 15, 2016 at 3:37 PM, James Starlight 
> wrote:
>
>> Dear Gromacs users!
>>
>> I am looking for some tutorial for the MARTINI simulation of
>> protein-protein recognition dealing with the big membrane protein
>> simulated within the membrane and its assosiation with the small water
>> soluble protein. The question - is it possible in existing Martini
>> system conisdted of only membrane protein solvated in membrane with
>> water to
>> i) increase box size on Z
>> ii)add some water
>> iii) put another water soluble protein in new space (on the distance
>> of the initial membrane protein complex)
>> iv) edit topology of new system and run new md
>>
>> assuming that i,ii and iv are trivial the problem here is the iii step :-)
>>
>> or alternatively if I would like to run new simulation with those 2
>> proteins (in the unbound form) how I can prepare such complex system
>> consisted of big protein in membrane plus water soluble protein
>> unbound from it?
>>
>> Thanks!
>>
>> Gleb
>> --
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Re: [gmx-users] Osmotic pressure

[Justin Lemkul]

On 4/18/16 4:43 AM, gozde ergin wrote:

In Roux study they did 10 independent 1.5 ns production simulation and I did 15 
ns simulation and divided it to 10 1.5ns simulations.

Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
   Roux study 300(+/- 10  bar)
   Experiment 300 bar


Your fluctuation seems unreasonably low.  Is this still with Berendsen?  If so, 
repeat it using Parrinello-Rahman for the barostat.  This result should be quite 
reproducible when using the method described exactly in the paper.


-Justin


On 18 Apr 2016, at 10:29, Mark Abraham  wrote:

Hi,

What statistical error do you (and they) measure? How many replicates have
each of you done?

Mark

On Mon, 18 Apr 2016 10:25 gozde ergin  wrote:


Hi Justin,

I corrected the nonbonded settings as your suggestion ;

; Bond parameters
continuation = no
constraint_algorithm = shake
constraints  = h-bonds
shake_tol= 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Neighborsearching
ns_type = grid
nstlist = 5
rlist   = 1.2
rcoulomb= 1.2
rvdw= 1.2

However my osmotic pressure result is still far from the Luo 2010
study.
I have the same number of Na Cl ions and water molecules. I run the
simulation for 15ns.
System size is the same, water model and force field are the same as Roux
study.
Basically I should get the same result.
Here is the result,

Osmotic pressure for 5M : My result 217 bar
  Roux study ~300 bar

Any suggestions would be appreciated.


On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:



On 4/15/16 5:20 AM, gozde ergin wrote:

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt

concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
molecules.

I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and

use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
pressure.

Actually I try to get the similar results as Lou 2010 study.

However my osmotic pressure results are on the line of ideal solution

osmotic pressure as shown equation in below;


P = cRT (Van’t Hoff equation)

but not the similar result with experiments.



What values do you actually get?  How do they compare with the values

from the Roux paper?  Are you remembering to divide by 2*area in your
calculation (since you have two walls)?



Is there anyone here that get the same trend as me for osmotic pressure

calculation? Or is there something that I miss?



Here is my .mdp file;

define   = -DPOSRES
integrator   = md
dt   = 0.002
nsteps   = 250   ;
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no;
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ;
nstlist = 5 ;
rlist   = 1.1   ;
rcoulomb= 1.1   ;
rvdw= 1.1   ;


These nonbonded settings are wrong.  The values for CHARMM36 are well

established and you should not deviate from them.


http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>


-Justin


; Electrostatics
coulombtype = PME   ;
pme_order   = 4 ;
fourierspacing  = 0.16  ;

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also

weak coupling

pcoupltype  = semiisotropic ; uniform scaling of x-y-z box

vectors

tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility,

bar^-1

refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System




--
==

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

Re: [gmx-users] position restrain energy

[Justin Lemkul]

On 4/18/16 9:05 AM, Nikhil Maroli wrote:

Hi thanks for your suggestion,

When i give both same name in mdp and top it gives an error

Atom index (123) in position_restraints out of bounds (1-122).
This probably means that you have inserted topology section "position_restraints


this is my topology file structure
; Include forcefield parameters
#include "toppar/charmm36.itp"

#include "toppar/PROA.itp"
#include "toppar/PROB.itp"
#include "toppar/PROC.itp"
#include "toppar/PROD.itp"
#include "toppar/PROE.itp"
#include "toppar/PROF.itp"
#include "toppar/PROG.itp"
#include "toppar/PROH.itp"
; Ligand position restraints
#ifdef POSRES_PROT
#include "posre_cpn.itp"
#endif



You can't do this.  Restraints are applied on a per-moleculetype basis.

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds


#include "toppar/POPE.itp"
#include "toppar/TIP3.itp"
#include "toppar/SOD.itp"
#include "toppar/CLA.itp"



PROAPROH  are identical cyclic peptide rings ,posre_cpn is restrain file
for c-alpha atoms in all the rings .

in mpd file
define  = -DPOSRES_PROT

when i give only
define  = -DPOSRES

in mdp grompp running successfully but in gmx energy no restrain energy --



Because it's doing precisely nothing, so no error can be raised and no 
restraints are applied because of the mismatch between define and #ifdef.


-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] MARTINI simulation of protein-protein recognition

[James Starlight]

It seems like smth very complicated :)

I just need to put two different proteins in the system - one in the
membrane (A) and one in the water (B) and simulate it independently 10
times to collect statistics about associations of A and B during those
runs. The problems that I don't know how to put 2 different unbound
proteins in the MARTINI system.

James

2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
> Hi,
>
> I assume you want to study the binding of your water soluble protein to
> your membrane(protein). DAFT was created to do just this. DOI:
> 10.1021/ct5010092
>
> Peter
>
> On Fri, Apr 15, 2016 at 3:37 PM, James Starlight 
> wrote:
>
>> Dear Gromacs users!
>>
>> I am looking for some tutorial for the MARTINI simulation of
>> protein-protein recognition dealing with the big membrane protein
>> simulated within the membrane and its assosiation with the small water
>> soluble protein. The question - is it possible in existing Martini
>> system conisdted of only membrane protein solvated in membrane with
>> water to
>> i) increase box size on Z
>> ii)add some water
>> iii) put another water soluble protein in new space (on the distance
>> of the initial membrane protein complex)
>> iv) edit topology of new system and run new md
>>
>> assuming that i,ii and iv are trivial the problem here is the iii step :-)
>>
>> or alternatively if I would like to run new simulation with those 2
>> proteins (in the unbound form) how I can prepare such complex system
>> consisted of big protein in membrane plus water soluble protein
>> unbound from it?
>>
>> Thanks!
>>
>> Gleb
>> --
>> Gromacs Users mailing list
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[gmx-users] wierd gro file output.

[abhishek khetan]

Dear gmx-users,

I was analysing some trajectory files from a box of acetonitrile solvents
when i realised that despite using trjconv -pbc whole and then trjconv -pbc
no jump, the molecules appeared to be broken when visualising using pymol.

When i looked that the gro file, the final gro file was of the kind:

ACN216
 1296
1ACN C11   0.030   0.065   2.621
2ACN H22   0.110   0.009   2.572
3ACN H33  -0.006   0.008   2.706
4ACN H44  -0.052   0.080   2.550
5ACN C55   0.080   0.195   2.666
6ACN N66   0.120   0.298   2.702
1ACN C17   1.963   1.695   0.110
2ACN H28   2.012   1.649   0.196
3ACN H39   1.866   1.647   0.095
4ACN H4   10   2.024   1.681   0.021
5ACN C5   11   1.944   1.838   0.136
6ACN N6   12   1.928   1.951   0.157
1ACN C1   13   0.033   2.237   2.583
2ACN H2   14   0.129   2.281   2.609
3ACN H3   15  -0.009   2.290   2.497
4ACN H4   16  -0.035   2.247   2.667
 
 

Where as the input file at the beginning of the simulations had the form

GROup of MAchos and Cynical Suckers
 1296
1ACN C11   0.000  -0.117   0.000
1ACN H22   0.102  -0.154   0.000
1ACN H33  -0.051  -0.154   0.089
1ACN H44  -0.051  -0.154  -0.089
1ACN C55   0.000   0.028   0.000
1ACN N66   0.000   0.143   0.000
2ACN C17   2.050   1.716   0.214
2ACN H28   2.149   1.683   0.242
2ACN H39   1.984   1.707   0.300
2ACN H4   10   2.012   1.653   0.134
2ACN C5   11   2.054   1.855   0.169
2ACN N6   12   2.058   1.964   0.135
3ACN C1   13   2.580   2.268   2.635
3ACN H2   14   2.667   2.329   2.609
3ACN H3   15   2.506   2.278   2.557
3ACN H4   16   2.539   2.304   2.729

As you can see the output gro file has teh residue numbeing gobbled up,
although in a very orderly manner. Could you please suggest whats going on.
I was hoping that using -pbc whole would not make any difference because
none of the bond would be broken in my simulations. However, even after
using -pbc whole in the trjconv routine, I find molecules broken

Thanks for the help in advance.

-- 
MfG,
abhishek
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Re: [gmx-users] position restrain energy

[Nikhil Maroli]

Hi thanks for your suggestion,

When i give both same name in mdp and top it gives an error

Atom index (123) in position_restraints out of bounds (1-122).
This probably means that you have inserted topology section "position_restraints


this is my topology file structure
; Include forcefield parameters
#include "toppar/charmm36.itp"

#include "toppar/PROA.itp"
#include "toppar/PROB.itp"
#include "toppar/PROC.itp"
#include "toppar/PROD.itp"
#include "toppar/PROE.itp"
#include "toppar/PROF.itp"
#include "toppar/PROG.itp"
#include "toppar/PROH.itp"
; Ligand position restraints
#ifdef POSRES_PROT
#include "posre_cpn.itp"
#endif

#include "toppar/POPE.itp"
#include "toppar/TIP3.itp"
#include "toppar/SOD.itp"
#include "toppar/CLA.itp"



PROAPROH  are identical cyclic peptide rings ,posre_cpn is restrain file
for c-alpha atoms in all the rings .

in mpd file
define  = -DPOSRES_PROT

when i give only
define  = -DPOSRES

in mdp grompp running successfully but in gmx energy no restrain energy --




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Re: [gmx-users] Zn moves away from protein - ligand complex

[Mark Abraham]

Hi,

If you have a cluster of things that make sense to treat together then you
must tell the tool that, via using such an index group. We haven't yet
worked out to implement "do what I want" :-)

Mark

On Mon, 18 Apr 2016 13:40 HongTham  wrote:

> Hello Gromacs users,
> I'm running a Zn bound protein - ligand complex simulation. I solvated
> whole system in a dodecahedron box. I also meet the problems with boundary
> effects. I try to use the gmx trjconv with option -pbc mol -ur compact
> -center to fix the problem. However, it doesn't work. The protein and
> ligand was centered to the water box, but not Zn ion.
> In some frame, Zn stay in the active site, sometime, it appear out site of
> the active site. I use VMD and display the system with many box (not only
> one unit), and see ZN till stay in the active site, but that is Zn of
> neighbor box, not the current box. its Zn ion now is stay in the active
> site of another box.
> I also tried with many option (cluster, nojump, -fit rot+trans) or change
> the selection of centering but they all useless. The -pbc nojump seems to
> be fine , it makes the protein + ligand + Zn stay together, but the water
> molecules are definitely distracted. It is difficult for me to calculate
> the water molecules within 0.5 to 10 nm of Zn and ligand.
> Anyone has been same situation with me? Would anyone give me a suggestion
> to fix that problem.
> Thank you so much.
> Best regards,
> Hongtham
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Re: [gmx-users] Thermodynamic integration

[Hannes Loeffler]

TI/FEP are appropriate when you have "small" changes between states.
Whether you delete/create all of a molecule or just part of it doesn't
matter that much.  So a relative simulation between a glycated and
non-glycated sounds quite reasonable to me.  Of course, this will become
increasingly more difficult with increasing chain length of
carbohydrates but you could do in additional steps if necessary.  What
is important is that you draw up a proper thermodynamic cycle to ensure
that you really calculate what you want to.

On Mon, 18 Apr 2016 11:06:40 +
"Nash, Anthony"  wrote:

> Hi Mark,
> 
> I will give that a thorough read. I was wondering if you could
> possibly comment on whether TI is an appropriate tool for calculating
> the free energy difference between two states, A―> non-glycated side
> chain, and b―> glycated side chain? Most examples given focus on the
> inclusion/exclusion of some small molecule in some large system.
> 
> I have tried umbrella sampling and although my results are extremely
> interesting, I’ve had to manipulate the initial systems to take it
> from a crystal structure with defined periodicity in x-y-z
> dimensions, to a slab in the x-y plane, and a water bath in the z
> plane. 
> 
> Thanks
> Anthony 
> 
> 
> 
> 
> On 18/04/2016 11:53,
> "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark
> Abraham"  of mark.j.abra...@gmail.com> wrote:
> 
> >Hi,
> >
> >Also you might consider pmx
> >http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such
> >topology generation. There is further work in the pipeline, so do
> >get in touch with Bert if there's something of interest.
> >
> >Mark
> >
> >On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony 
> >wrote:
> >
> >> From the site, “..or the free energy of a mutation of a side
> >> chain.”
> >>
> >> I think this is what I am after. Many thanks for the link.
> >>
> >> Anthony
> >>
> >>
> >>
> >> On 18/04/2016 10:42,
> >> "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >>on
> >> behalf of Hannes Loeffler"
> >>  >> hannes.loeff...@stfc.ac.uk> wrote:
> >>
> >> >A good starting point is http://www.alchemistry.org/ which has
> >> >quite a lot of detail on relative alchemical free energy
> >> >simulations (not only TI).
> >> >
> >> >On Mon, 18 Apr 2016 09:27:02 +
> >> >"Nash, Anthony"  wrote:
> >> >
> >> >> Hi all,
> >> >>
> >> >> I¹m looking for a guide on performing TI between a protein in
> >> >> its crystal periodicity with a particular residue (state A), to
> >> >> the same system but with a different residue (state B).
> >> >>
> >> >> I¹m currently using
> >> >>
> >> >>
> >> 
> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/fr
> >> >>ee
> >> >> _energy/01_theory.html as a guide, however this is more, if I
> >> >> understand having read through it, on the presence-to-absence of
> >> >> methane in a water solvent rather than a replacement with
> >> >> something else.
> >> >>
> >> >> I haven¹t had too much luck googling and I¹m looking piecemeal
> >> >> through the manual with little success.
> >> >>
> >> >> Thanks
> >> >> Anthony
> >> >>
> >> >>
> >> >>
> >> >
> >> >--
> >> >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] Zn moves away from protein - ligand complex

[HongTham]

Hello Gromacs users,
I'm running a Zn bound protein - ligand complex simulation. I solvated
whole system in a dodecahedron box. I also meet the problems with boundary
effects. I try to use the gmx trjconv with option -pbc mol -ur compact
-center to fix the problem. However, it doesn't work. The protein and
ligand was centered to the water box, but not Zn ion.
In some frame, Zn stay in the active site, sometime, it appear out site of
the active site. I use VMD and display the system with many box (not only
one unit), and see ZN till stay in the active site, but that is Zn of
neighbor box, not the current box. its Zn ion now is stay in the active
site of another box.
I also tried with many option (cluster, nojump, -fit rot+trans) or change
the selection of centering but they all useless. The -pbc nojump seems to
be fine , it makes the protein + ligand + Zn stay together, but the water
molecules are definitely distracted. It is difficult for me to calculate
the water molecules within 0.5 to 10 nm of Zn and ligand.
Anyone has been same situation with me? Would anyone give me a suggestion
to fix that problem.
Thank you so much.
Best regards,
Hongtham
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Re: [gmx-users] Thermodynamic integration

[Nash, Anthony]

Hi Mark,

I will give that a thorough read. I was wondering if you could possibly
comment on whether TI is an appropriate tool for calculating the free
energy difference between two states, A―> non-glycated side chain, and b―>
glycated side chain? Most examples given focus on the inclusion/exclusion
of some small molecule in some large system.

I have tried umbrella sampling and although my results are extremely
interesting, I’ve had to manipulate the initial systems to take it from a
crystal structure with defined periodicity in x-y-z dimensions, to a slab
in the x-y plane, and a water bath in the z plane.
 

Thanks
Anthony 




On 18/04/2016 11:53, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>Also you might consider pmx
>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
>generation. There is further work in the pipeline, so do get in touch with
>Bert if there's something of interest.
>
>Mark
>
>On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony  wrote:
>
>> From the site, “..or the free energy of a mutation of a side chain.”
>>
>> I think this is what I am after. Many thanks for the link.
>>
>> Anthony
>>
>>
>>
>> On 18/04/2016 10:42, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Hannes Loeffler"
>> > hannes.loeff...@stfc.ac.uk> wrote:
>>
>> >A good starting point is http://www.alchemistry.org/ which has quite a
>> >lot of detail on relative alchemical free energy simulations (not only
>> >TI).
>> >
>> >On Mon, 18 Apr 2016 09:27:02 +
>> >"Nash, Anthony"  wrote:
>> >
>> >> Hi all,
>> >>
>> >> I¹m looking for a guide on performing TI between a protein in its
>> >> crystal periodicity with a particular residue (state A), to the same
>> >> system but with a different residue (state B).
>> >>
>> >> I¹m currently using
>> >>
>> >>
>> 
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/fr
>> >>ee
>> >> _energy/01_theory.html as a guide, however this is more, if I
>> >> understand having read through it, on the presence-to-absence of
>> >> methane in a water solvent rather than a replacement with something
>> >> else.
>> >>
>> >> I haven¹t had too much luck googling and I¹m looking piecemeal
>> >> through the manual with little success.
>> >>
>> >> Thanks
>> >> Anthony
>> >>
>> >>
>> >>
>> >
>> >--
>> >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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Re: [gmx-users] Dihedral convention

[Mark Abraham]

Hi,
On Thu, 14 Apr 2016 21:10 Christopher Neale 
wrote:

> Where? I took a look at v5.1.2 manual section 4.2.12 and could not find
> it, hence my suggestion to test it out. I note that there is indeed some
> definition in section 4.2.13: "Proper dihedral angles are defined according
> to the IUPAC/IUB convention, where φ is the angle
> between the ijk and the jkl planes, with zero corresponding to the cis
> configuration (i and l onthe same side)." -- but that specifies that it
> relates to propers


Impropers are defined in the previous section, which refers to the one you
quote, where phi is defined clearly.


> and also it doesn't exactly answer the OP's question about ranges from
> 0-360 or -180 to +180.


This doesn't matter at all. cos(n * phi + phi_0) is invariant under any
increment to phi or phi_0 by an increment of a multiple of a full rotation,
because n is an integer.


> Everything is also complicated by the RB definition "where ψ = φ − 180◦",
> so now it is clear that an "angle" does not always have the same definition.
>

That's life. RB has its roots in the polymer simulation community, who use
a different convention from biomolecular folks. I'm open to ways to improve
the wording, though.

Mark


> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 14 April 2016 14:44
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Dihedral convention
>
> Hi,
>
> Also, the details of angle conventions are all covered in the reference
> manual.
>
> Mark
>
> On Thu, 14 Apr 2016 20:37 Christopher Neale 
> wrote:
>
> > Make a box with a single molecule of n-butane, no pressure coupling or
> > pme, use the sd integrator, test it out?
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Parvez
> Mh
> > 
> > Sent: 14 April 2016 12:47
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Dihedral convention
> >
> > Dr. Lemkul,
> >
> > I understand what you said. My question is, in function type 2 ,there are
> > two parameters 1) force constant and 2) angle of plane. For angle
> > measurement, which convention does gromacs follow, -180 t0 180 or 0 to
> 360?
> >
> > --Masrul
> >
> > On Wed, Apr 13, 2016 at 8:35 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 4/13/16 8:29 PM, Parvez Mh wrote:
> > >
> > >> I am talking about improper dihedral function type 2.
> > >>
> > >>
> > > Impropers are intended to keep planar groups planar, not to restrict
> > other
> > > geometries.  You would be better off with a normal dihedral restraint
> or
> > > potentially figuring out why your force field isn't preserving the
> > desired
> > > geometry.
> > >
> > > -Justin
> > >
> > >
> > > --Masrul
> > >>
> > >> On Wed, Apr 13, 2016 at 7:21 PM, Justin Lemkul 
> wrote:
> > >>
> > >>
> > >>>
> > >>> On 4/13/16 2:51 PM, Parvez Mh wrote:
> > >>>
> > >>> Dear all:
> > 
> >  I would like to  use a harmonic type potential for dihedral. Should
> i
> >  use
> >  angle value (-180 to 180 ) or (0 to 360) convention. My equilibrium
> >  angle
> >  is -64 degree. then what would be the angle -64 or (-64+360=)296
> > degree?
> > 
> > 
> >  Unless you're writing your own code for new functions, there is no
> > such
> > >>> thing as a harmonic dihedral.  See the manual, Chapter 4, for
> available
> > >>> functional forms.
> > >>>
> > >>> -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
> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>> send a mail to gmx-users-requ...@gromacs.org.
> > >>>
> > >>>
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health 

Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Off-list Ali sent me a link to his movie - this does indeed show the ligand
diffusing out gradually, rather than "jumping" in a discrete step. Such an
event would be very rare for a lot of bound ligands with a suitable model
physics, so if it's reproducible then you have problems with the model,
somehow.

Mark

On Fri, Apr 15, 2016 at 3:30 PM Mark Abraham 
wrote:

> Hi,
>
> Please see
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
> On Fri, Apr 15, 2016 at 12:22 PM ali osouli 
> wrote:
>
>> Dear all
>> My MD run movie shows that my ligand jump out of protein in the early
>> picoseconds of simulation, does anybody knwos which step of my MD should i
>> check?
>> In additon to rutin steps i have included a distance restraint file to
>> topolgy.itp.
>> Best regards Ali
>> --
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] Thermodynamic integration

[Mark Abraham]

Hi,

Also you might consider pmx
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
generation. There is further work in the pipeline, so do get in touch with
Bert if there's something of interest.

Mark

On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony  wrote:

> From the site, “..or the free energy of a mutation of a side chain.”
>
> I think this is what I am after. Many thanks for the link.
>
> Anthony
>
>
>
> On 18/04/2016 10:42, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Hannes Loeffler"
>  hannes.loeff...@stfc.ac.uk> wrote:
>
> >A good starting point is http://www.alchemistry.org/ which has quite a
> >lot of detail on relative alchemical free energy simulations (not only
> >TI).
> >
> >On Mon, 18 Apr 2016 09:27:02 +
> >"Nash, Anthony"  wrote:
> >
> >> Hi all,
> >>
> >> I¹m looking for a guide on performing TI between a protein in its
> >> crystal periodicity with a particular residue (state A), to the same
> >> system but with a different residue (state B).
> >>
> >> I¹m currently using
> >>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/fr
> >>ee
> >> _energy/01_theory.html as a guide, however this is more, if I
> >> understand having read through it, on the presence-to-absence of
> >> methane in a water solvent rather than a replacement with something
> >> else.
> >>
> >> I haven¹t had too much luck googling and I¹m looking piecemeal
> >> through the manual with little success.
> >>
> >> Thanks
> >> Anthony
> >>
> >>
> >>
> >
> >--
> >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] Thermodynamic integration

[Hannes Loeffler]

A good starting point is http://www.alchemistry.org/ which has quite a
lot of detail on relative alchemical free energy simulations (not only
TI).

On Mon, 18 Apr 2016 09:27:02 +
"Nash, Anthony"  wrote:

> Hi all,
> 
> I¹m looking for a guide on performing TI between a protein in its
> crystal periodicity with a particular residue (state A), to the same
> system but with a different residue (state B).
> 
> I¹m currently using
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free
> _energy/01_theory.html as a guide, however this is more, if I
> understand having read through it, on the presence-to-absence of
> methane in a water solvent rather than a replacement with something
> else.
> 
> I haven¹t had too much luck googling and I¹m looking piecemeal
> through the manual with little success.
> 
> Thanks
> Anthony  
> 
> 
> 

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[gmx-users] Thermodynamic integration

[Nash, Anthony]

Hi all,

I¹m looking for a guide on performing TI between a protein in its crystal
periodicity with a particular residue (state A), to the same system but
with a different residue (state B).

I¹m currently using
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free
_energy/01_theory.html as a guide, however this is more, if I understand
having read through it, on the presence-to-absence of methane in a water
solvent rather than a replacement with something else.

I haven¹t had too much luck googling and I¹m looking piecemeal through the
manual with little success.

Thanks
Anthony  



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Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Mark,

I guess so because a lot of studies cite this study also their results are 
almost identical with the experimental one.

> On 18 Apr 2016, at 10:46, Mark Abraham  wrote:
> 
> Are they known to produce these observables accurately

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Re: [gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

Are they known to produce these observables accurately? Might a wrong
distribution of KE affect them?

Mark

On Fri, 15 Apr 2016 12:00 gozde ergin  wrote:

> Hi Mark,
>
> I use Berendsen for T and P-coupl.
> Do you think I should change them?
>
> > On 15 Apr 2016, at 11:55, Mark Abraham  wrote:
> >
> > Hi,
> >
> > Also you can choose coupling algorithms that are known to sample correct
> > ensembles...
> >
> > Mark
> >
> > On Fri, 15 Apr 2016 11:50 Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/15/16 5:20 AM, gozde ergin wrote:
> >>> Dear all,
> >>>
> >>> I simulate the NaCl solution to estimate the osmotic pressure. My salt
> >> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> >> molecules.
> >>> I use CHARMM36 ff with NBFIX correction.
> >>>
> >>> After the simulation I extract the z-coordinates of restraint ions and
> >> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the
> osmotic
> >> pressure.
> >>> Actually I try to get the similar results as Lou 2010 study.
> >>>
> >>> However my osmotic pressure results are on the line of ideal solution
> >> osmotic pressure as shown equation in below;
> >>>
> >>> P = cRT (Van’t Hoff equation)
> >>>
> >>> but not the similar result with experiments.
> >>>
> >>
> >> What values do you actually get?  How do they compare with the values
> from
> >> the
> >> Roux paper?  Are you remembering to divide by 2*area in your calculation
> >> (since
> >> you have two walls)?
> >>
> >>> Is there anyone here that get the same trend as me for osmotic pressure
> >> calculation? Or is there something that I miss?
> >>>
> >>>
> >>> Here is my .mdp file;
> >>>
> >>> define   = -DPOSRES
> >>> integrator   = md
> >>> dt   = 0.002
> >>> nsteps   = 250   ;
> >>> ; Output control
> >>> nstxout  = 2000
> >>> nstvout  = 2000
> >>> nstlog   = 2000
> >>> nstenergy= 2000
> >>> ; Bond parameters
> >>> continuation = no;
> >>> constraint_algorithm = shake ; h
> >>> constraints  = all-bonds ; a
> >>> shake_tol= 0.0001
> >>> ; Neighborsearching
> >>> ns_type = grid  ;
> >>> nstlist = 5 ;
> >>> rlist   = 1.1   ;
> >>> rcoulomb= 1.1   ;
> >>> rvdw= 1.1   ;
> >>
> >> These nonbonded settings are wrong.  The values for CHARMM36 are well
> >> established and you should not deviate from them.
> >>
> >> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
> >>
> >> -Justin
> >>
> >>> ; Electrostatics
> >>> coulombtype = PME   ;
> >>> pme_order   = 4 ;
> >>> fourierspacing  = 0.16  ;
> >>>
> >>> tcoupl   = berendsen
> >>> tc-grps  = System
> >>> tau_t= 1.0
> >>> ref_t= 300
> >>> ; Pressure coupling is on
> >>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> >> weak coupling
> >>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
> >> vectors
> >>> tau_p   = 2.0 2.0  ; time constant, in ps
> >>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
> >>> compressibility = 0 4.5e-5; isothermal compressibility,
> >> bar^-1
> >>> refcoord_scaling= com
> >>> ; Periodic boundary conditions
> >>> pbc = xyz   ; 3-D PBC
> >>> ; Dispersion correction
> >>> DispCorr= EnerPres  ; account for cut-off vdW scheme
> >>> ; Velocity generation
> >>> gen_vel = yes   ; Velocity generation is on
> >>> gen_temp= 300   ; temperature for velocity generation
> >>> gen_seed= -1; random seed
> >>> ; COM motion removal
> >>> ; These options remove COM motion of the system
> >>> nstcomm = 10
> >>> comm-mode   = Linear
> >>> comm-grps   = System
> >>>
> >>>
> >>
> >> --
> >> ==
> >>
> >> 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
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to 

Re: [gmx-users] Osmotic pressure

[gozde ergin]

In Roux study they did 10 independent 1.5 ns production simulation and I did 15 
ns simulation and divided it to 10 1.5ns simulations.

Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
  Roux study 300(+/- 10  bar)
  Experiment 300 bar
> On 18 Apr 2016, at 10:29, Mark Abraham  wrote:
> 
> Hi,
> 
> What statistical error do you (and they) measure? How many replicates have
> each of you done?
> 
> Mark
> 
> On Mon, 18 Apr 2016 10:25 gozde ergin  wrote:
> 
>> Hi Justin,
>> 
>> I corrected the nonbonded settings as your suggestion ;
>> 
>> ; Bond parameters
>> continuation = no
>> constraint_algorithm = shake
>> constraints  = h-bonds
>> shake_tol= 0.0001
>> cutoff-scheme = Verlet
>> vdwtype = cutoff
>> vdw-modifier = force-switch
>> rvdw-switch = 1.0
>> ; Neighborsearching
>> ns_type = grid
>> nstlist = 5
>> rlist   = 1.2
>> rcoulomb= 1.2
>> rvdw= 1.2
>> 
>> However my osmotic pressure result is still far from the Luo 2010
>> study.
>> I have the same number of Na Cl ions and water molecules. I run the
>> simulation for 15ns.
>> System size is the same, water model and force field are the same as Roux
>> study.
>> Basically I should get the same result.
>> Here is the result,
>> 
>> Osmotic pressure for 5M : My result 217 bar
>>  Roux study ~300 bar
>> 
>> Any suggestions would be appreciated.
>> 
>>> On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 4/15/16 5:20 AM, gozde ergin wrote:
 Dear all,
 
 I simulate the NaCl solution to estimate the osmotic pressure. My salt
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
>> molecules.
 I use CHARMM36 ff with NBFIX correction.
 
 After the simulation I extract the z-coordinates of restraint ions and
>> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
>> pressure.
 Actually I try to get the similar results as Lou 2010 study.
 
 However my osmotic pressure results are on the line of ideal solution
>> osmotic pressure as shown equation in below;
 
 P = cRT (Van’t Hoff equation)
 
 but not the similar result with experiments.
 
>>> 
>>> What values do you actually get?  How do they compare with the values
>> from the Roux paper?  Are you remembering to divide by 2*area in your
>> calculation (since you have two walls)?
>>> 
 Is there anyone here that get the same trend as me for osmotic pressure
>> calculation? Or is there something that I miss?
 
 
 Here is my .mdp file;
 
 define   = -DPOSRES
 integrator   = md
 dt   = 0.002
 nsteps   = 250   ;
 ; Output control
 nstxout  = 2000
 nstvout  = 2000
 nstlog   = 2000
 nstenergy= 2000
 ; Bond parameters
 continuation = no;
 constraint_algorithm = shake ; h
 constraints  = all-bonds ; a
 shake_tol= 0.0001
 ; Neighborsearching
 ns_type = grid  ;
 nstlist = 5 ;
 rlist   = 1.1   ;
 rcoulomb= 1.1   ;
 rvdw= 1.1   ;
>>> 
>>> These nonbonded settings are wrong.  The values for CHARMM36 are well
>> established and you should not deviate from them.
>>> 
>>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
>>> 
>>> -Justin
>>> 
 ; Electrostatics
 coulombtype = PME   ;
 pme_order   = 4 ;
 fourierspacing  = 0.16  ;
 
 tcoupl   = berendsen
 tc-grps  = System
 tau_t= 1.0
 ref_t= 300
 ; Pressure coupling is on
 pcoupl  = Berendsen ; Pressure coupling on in NPT, also
>> weak coupling
 pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
>> vectors
 tau_p   = 2.0 2.0  ; time constant, in ps
 ref_p   = 1.0 1.0  ; reference pressure (in bar)
 compressibility = 0 4.5e-5; isothermal compressibility,
>> bar^-1
 refcoord_scaling= com
 ; Periodic boundary conditions
 pbc = xyz   ; 3-D PBC
 ; Dispersion correction
 DispCorr= EnerPres  ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel = yes   ; Velocity generation is on
 gen_temp= 300   ; temperature for velocity generation
 gen_seed= -1; random seed
 ; COM motion removal
 ; These options 

Re: [gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

What statistical error do you (and they) measure? How many replicates have
each of you done?

Mark

On Mon, 18 Apr 2016 10:25 gozde ergin  wrote:

> Hi Justin,
>
> I corrected the nonbonded settings as your suggestion ;
>
> ; Bond parameters
> continuation = no
> constraint_algorithm = shake
> constraints  = h-bonds
> shake_tol= 0.0001
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch
> rvdw-switch = 1.0
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist   = 1.2
> rcoulomb= 1.2
> rvdw= 1.2
>
> However my osmotic pressure result is still far from the Luo 2010
> study.
> I have the same number of Na Cl ions and water molecules. I run the
> simulation for 15ns.
> System size is the same, water model and force field are the same as Roux
> study.
> Basically I should get the same result.
> Here is the result,
>
> Osmotic pressure for 5M : My result 217 bar
>   Roux study ~300 bar
>
> Any suggestions would be appreciated.
>
> > On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
> >
> >
> >
> > On 4/15/16 5:20 AM, gozde ergin wrote:
> >> Dear all,
> >>
> >> I simulate the NaCl solution to estimate the osmotic pressure. My salt
> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> molecules.
> >> I use CHARMM36 ff with NBFIX correction.
> >>
> >> After the simulation I extract the z-coordinates of restraint ions and
> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
> pressure.
> >> Actually I try to get the similar results as Lou 2010 study.
> >>
> >> However my osmotic pressure results are on the line of ideal solution
> osmotic pressure as shown equation in below;
> >>
> >> P = cRT (Van’t Hoff equation)
> >>
> >> but not the similar result with experiments.
> >>
> >
> > What values do you actually get?  How do they compare with the values
> from the Roux paper?  Are you remembering to divide by 2*area in your
> calculation (since you have two walls)?
> >
> >> Is there anyone here that get the same trend as me for osmotic pressure
> calculation? Or is there something that I miss?
> >>
> >>
> >> Here is my .mdp file;
> >>
> >> define   = -DPOSRES
> >> integrator   = md
> >> dt   = 0.002
> >> nsteps   = 250   ;
> >> ; Output control
> >> nstxout  = 2000
> >> nstvout  = 2000
> >> nstlog   = 2000
> >> nstenergy= 2000
> >> ; Bond parameters
> >> continuation = no;
> >> constraint_algorithm = shake ; h
> >> constraints  = all-bonds ; a
> >> shake_tol= 0.0001
> >> ; Neighborsearching
> >> ns_type = grid  ;
> >> nstlist = 5 ;
> >> rlist   = 1.1   ;
> >> rcoulomb= 1.1   ;
> >> rvdw= 1.1   ;
> >
> > These nonbonded settings are wrong.  The values for CHARMM36 are well
> established and you should not deviate from them.
> >
> > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
> >
> > -Justin
> >
> >> ; Electrostatics
> >> coulombtype = PME   ;
> >> pme_order   = 4 ;
> >> fourierspacing  = 0.16  ;
> >>
> >> tcoupl   = berendsen
> >> tc-grps  = System
> >> tau_t= 1.0
> >> ref_t= 300
> >> ; Pressure coupling is on
> >> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> weak coupling
> >> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
> vectors
> >> tau_p   = 2.0 2.0  ; time constant, in ps
> >> ref_p   = 1.0 1.0  ; reference pressure (in bar)
> >> compressibility = 0 4.5e-5; isothermal compressibility,
> bar^-1
> >> refcoord_scaling= com
> >> ; Periodic boundary conditions
> >> pbc = xyz   ; 3-D PBC
> >> ; Dispersion correction
> >> DispCorr= EnerPres  ; account for cut-off vdW scheme
> >> ; Velocity generation
> >> gen_vel = yes   ; Velocity generation is on
> >> gen_temp= 300   ; temperature for velocity generation
> >> gen_seed= -1; random seed
> >> ; COM motion removal
> >> ; These options remove COM motion of the system
> >> nstcomm = 10
> >> comm-mode   = Linear
> >> comm-grps   = System
> >>
> >>
> >
> > --
> > ==
> >
> > 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
> >
> > 

Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Justin,

I corrected the nonbonded settings as your suggestion ; 

; Bond parameters
continuation = no   
constraint_algorithm = shake 
constraints  = h-bonds 
shake_tol= 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Neighborsearching
ns_type = grid
nstlist = 5 
rlist   = 1.2   
rcoulomb= 1.2 
rvdw= 1.2  

However my osmotic pressure result is still far from the Luo 2010 study.
I have the same number of Na Cl ions and water molecules. I run the simulation 
for 15ns.
System size is the same, water model and force field are the same as Roux 
study. 
Basically I should get the same result.
Here is the result,

Osmotic pressure for 5M : My result 217 bar
  Roux study ~300 bar

Any suggestions would be appreciated.

> On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
> 
> 
> 
> On 4/15/16 5:20 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I simulate the NaCl solution to estimate the osmotic pressure. My salt 
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the 
>> molecules.
>> I use CHARMM36 ff with NBFIX correction.
>> 
>> After the simulation I extract the z-coordinates of restraint ions and use 
>> the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic 
>> pressure.
>> Actually I try to get the similar results as Lou 2010 study.
>> 
>> However my osmotic pressure results are on the line of ideal solution 
>> osmotic pressure as shown equation in below;
>> 
>> P = cRT (Van’t Hoff equation)
>> 
>> but not the similar result with experiments.
>> 
> 
> What values do you actually get?  How do they compare with the values from 
> the Roux paper?  Are you remembering to divide by 2*area in your calculation 
> (since you have two walls)?
> 
>> Is there anyone here that get the same trend as me for osmotic pressure 
>> calculation? Or is there something that I miss?
>> 
>> 
>> Here is my .mdp file;
>> 
>> define   = -DPOSRES
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 250   ;
>> ; Output control
>> nstxout  = 2000
>> nstvout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> ; Bond parameters
>> continuation = no;
>> constraint_algorithm = shake ; h
>> constraints  = all-bonds ; a
>> shake_tol= 0.0001
>> ; Neighborsearching
>> ns_type = grid  ;
>> nstlist = 5 ;
>> rlist   = 1.1   ;
>> rcoulomb= 1.1   ;
>> rvdw= 1.1   ;
> 
> These nonbonded settings are wrong.  The values for CHARMM36 are well 
> established and you should not deviate from them.
> 
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM 
> 
> 
> -Justin
> 
>> ; Electrostatics
>> coulombtype = PME   ;
>> pme_order   = 4 ;
>> fourierspacing  = 0.16  ;
>> 
>> tcoupl   = berendsen
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> ; Pressure coupling is on
>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
>> coupling
>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box 
>> vectors
>> tau_p   = 2.0 2.0  ; time constant, in ps
>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>> compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
>> refcoord_scaling= com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; Velocity generation is on
>> gen_temp= 300   ; temperature for velocity generation
>> gen_seed= -1; random seed
>> ; COM motion removal
>> ; These options remove COM motion of the system
>> nstcomm = 10
>> comm-mode   = Linear
>> comm-grps   = System
>> 
>> 
> 
> -- 
> ==
> 
> 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 
> 

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[Kroon, P.C.]

Hi,

I assume you want to study the binding of your water soluble protein to
your membrane(protein). DAFT was created to do just this. DOI:
10.1021/ct5010092

Peter

On Fri, Apr 15, 2016 at 3:37 PM, James Starlight 
wrote:

> Dear Gromacs users!
>
> I am looking for some tutorial for the MARTINI simulation of
> protein-protein recognition dealing with the big membrane protein
> simulated within the membrane and its assosiation with the small water
> soluble protein. The question - is it possible in existing Martini
> system conisdted of only membrane protein solvated in membrane with
> water to
> i) increase box size on Z
> ii)add some water
> iii) put another water soluble protein in new space (on the distance
> of the initial membrane protein complex)
> iv) edit topology of new system and run new md
>
> assuming that i,ii and iv are trivial the problem here is the iii step :-)
>
> or alternatively if I would like to run new simulation with those 2
> proteins (in the unbound form) how I can prepare such complex system
> consisted of big protein in membrane plus water soluble protein
> unbound from it?
>
> Thanks!
>
> Gleb
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] position restrain energy

[gozde ergin]

You defined in .top file as POSRES_Protein so in .mdp file you should call as   
  define  = -DPOSRES_Protein. 
The names in .top and .mdp should match


On 18 Apr 2016, at 08:46, Nikhil Maroli  wrote:
> 
> Dear all,
> i wanted to include position restrain to cyclic peptide nanotube c-alpha
> atoms,i have generated posre_cpn.itp file and added
> define  = -DPOSRES
> 
> in mdp file.
> and added in  .top as
> 
> #ifdef POSRES_Protein
> #include "posre_cpn.itp"
> #endif
> 
> 
> when i check with gmx energy i couldnt find an option for position restrain
> energy ,is my restrain is working ?!
> is it possible to know whether restrain is working or required increase
> before completing the full 100ns MD?
> 
> -- 
> Ragards,
> Nikhil Maroli
> -- 
> 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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> mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] on force field for ligand

[gozde ergin]

Hi Brett,

If you have all the necessary .itp files and if your .top file is generated 
correctly, yes it works.

> On 18 Apr 2016, at 09:23, Brett  wrote:
> 
> Dear All,
> 
> 
> Does GROMACS work if the force field for ligand part is GAFF force field?
> 
> 
> Brett
> -- 
> Gromacs Users mailing list
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[gmx-users] on force field for ligand

[Brett]

Dear All,


Does GROMACS work if the force field for ligand part is GAFF force field?


Brett
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[gmx-users] position restrain energy

[Nikhil Maroli]

Dear all,
i wanted to include position restrain to cyclic peptide nanotube c-alpha
atoms,i have generated posre_cpn.itp file and added
 define  = -DPOSRES

 in mdp file.
and added in  .top as

#ifdef POSRES_Protein
#include "posre_cpn.itp"
#endif


when i check with gmx energy i couldnt find an option for position restrain
energy ,is my restrain is working ?!
is it possible to know whether restrain is working or required increase
before completing the full 100ns MD?

-- 
Ragards,
Nikhil Maroli
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