[gmx-users] Correlation of dynamics between pairs of residues

[Ebert Maximilian]

Dear list,

I am looking for a tool in gromacs to generate a map of residues pairs to 
indicate wether the dynamic/movement is correlated or anti correlated. Which 
tool is able to generate such an output?

Thank you very much,

Max
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Re: [gmx-users] Correlation of dynamics between pairs of residues

[Ebert Maximilian]

Hi Justin,

thanks for your answer. gmx covar is really helpful and does what I was looking 
for.I have 3 replicates of the simulation and wanted now to compare the 
covariance and maybe calculate an average of the 3. The covara output is what I 
am looking for but the file created is more or less a picture and not really 
the data anymore. In addition, the scale of + and 0 nm^2 is not the same in 
each of the 3 output of the simulation so it is hard to compare. Is there a way 
to set min and max values for nm^2? Can I find an explanation how the data was 
calculated using the dat file i can generate using gmx covar? 

Thank you very much,

Max 


> On Mar 12, 2015, at 8:58 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 3/12/15 6:20 PM, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I am looking for a tool in gromacs to generate a map of residues pairs to 
>> indicate wether the dynamic/movement is correlated or anti correlated. Which 
>> tool is able to generate such an output?
>> 
> 
> gmx covar will plot the covariance matrix for all atom pairs (3N x 3N), but 
> you can map that to residues.
> 
> -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] Correlation of dynamics between pairs of residues

[Ebert Maximilian]

Thanks for taking the time to answer. However, I don’t really understand why 
having the same axis basically (so from -2 to 2 nm^2 for example) would defy 
the purpose of the analysis. Could you explain that? 

I guess your hint with open source is that i could check how the covara is 
calculated and do it on my own using the .dat ascii file? Do you know where the 
function is in the code?

Thanks,

Max

> On Mar 23, 2015, at 9:05 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 3/23/15 3:43 PM, Ebert Maximilian wrote:
>> Hi Justin,
>> 
>> thanks for your answer. gmx covar is really helpful and does what I was
>> looking for.I have 3 replicates of the simulation and wanted now to compare
>> the covariance and maybe calculate an average of the 3. The covara output is
>> what I am looking for but the file created is more or less a picture and not
>> really the data anymore. In addition, the scale of + and 0 nm^2 is not the
>> same in each of the 3 output of the simulation so it is hard to compare. Is
>> there a way to set min and max values for nm^2? Can I find an explanation how
>> the data was calculated using the dat file i can generate using gmx covar?
>> 
> 
> One approach would be to simply pool the trajectories and run gmx covar once. 
> That will do the analysis over all of your trajectories and you no longer 
> have this issue.  But there is no way to control what the min and max values 
> are; that sort of defeats the purpose of the analysis.
> 
> As for the explanation, that's why GROMACS is open source :)
> 
> -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] Checking the existence of a hydrogen bond network

[Ebert Maximilian]

Dear list,

I am trying to find a possibility with standard gromacs tools to verify in 
every frame if two residues are interconnected through a hbonds with a water 
molecule. My initial idea was to evaluate the hbonds of both residues per frame 
and write a small bash script looking for frames in which both residues hbonded 
with the same water molecule. However, I could’t find an option in gmx hbond to 
write out the hbonds per frame except for the number of hbonds per frame and a 
file with all partners. Before starting to have to loop over every frame 
individually and start gmx hbond as often as the number of frames I wanted to 
know if there is an easier approach to what I want to do.

Basically I want to know how long this bridge existed over the course of the 
simulation.

Thank you very much,

Max
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Re: [gmx-users] Checking the existence of a hydrogen bond network

[Ebert Maximilian]

Hey Erik,

Just wanted to thank you. This is exactly what I was looking for. Never looked 
at the end of the ndx file. Just a question regarding the index. If I am not 
mistaken the first entry of bond registry entry:

[ hbonds_Water-r_216_r_244 ]
   4216   4217   3342
   7225   7226   2962

should correspond to the last entry in the xpm file matrix:

/* y-axis:  0 1 2 3 4 5 6 7 8 9 10 11 12 */
" oo o  ooo oo  oo  ooo ooo ooo o oo  o   o ooo ooo oo   oo 
o “,
"oo 
  “


and hence the last bond entry (7225   7226   2962) corresponds to the line 
beneath the y-axis entry? Just to be sure.

Have a great day,

Max

> On Apr 16, 2015, at 11:28 AM, Erik Marklund  
> wrote:
> 
> Dear Max,
> 
> You will need to use the -hbm and -hbn options to generate the existance 
> function for all hydrogen bonds over time. Parsing those files requires a bit 
> of work, but is certainly doable.
> 
> Kind regards,
> Erik
> 
>> On 16 Apr 2015, at 12:59, Ebert Maximilian  wrote:
>> 
>> Dear list,
>> 
>> I am trying to find a possibility with standard gromacs tools to verify in 
>> every frame if two residues are interconnected through a hbonds with a water 
>> molecule. My initial idea was to evaluate the hbonds of both residues per 
>> frame and write a small bash script looking for frames in which both 
>> residues hbonded with the same water molecule. However, I could’t find an 
>> option in gmx hbond to write out the hbonds per frame except for the number 
>> of hbonds per frame and a file with all partners. Before starting to have to 
>> loop over every frame individually and start gmx hbond as often as the 
>> number of frames I wanted to know if there is an easier approach to what I 
>> want to do.
>> 
>> Basically I want to know how long this bridge existed over the course of the 
>> simulation.
>> 
>> Thank you very much,
>> 
>> Max
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[gmx-users] Can't find the reference in hbond calculation between the map and the index file

[Ebert Maximilian]

Hey List,

I already got a nice idea from Erik how to find residues bridged by a water 
molecule by using the hbond tool and the map and index file. I still have a 
question regarding the index. If I am not mistaken the first entry of bond 
registry entry:

[ hbonds_Water-r_216_r_244 ]
  4216   4217   3342
  7225   7226   2962

should correspond to the last entry in the xpm file matrix:

/* y-axis:  0 1 2 3 4 5 6 7 8 9 10 11 12 */
" oo o  ooo oo  oo  ooo ooo ooo o oo  o   o ooo ooo oo   oo 
o “,
"oo 
  “


and hence the last bond entry (7225   7226   2962) corresponds to the line 
beneath the y-axis entry? Just to be sure. Is this correct? Couldn’t find any 
hint what is described by Hydrogen Bond Index in the map file.

Thank you very much,

Max
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Re: [gmx-users] Can't find the reference in hbond calculation between the map and the index file

[Ebert Maximilian]

Hey Justin,

Thank you for your answer. I wanted just to be sure since other programs define 
H-bonds slightly different so identification of each line is a bit complicated 
when comparing frame by frame. I was trying to find the exact same number of 
H-bonds for instance in pymol but I could never get the definition about right 
so that gromacs and pymol find exactly the same hbonds.

thanks for the offer I also wrote a program now to determine hydrogen bond 
networks across one water molecule. not sure if this can be any helpful to 
anyone. if so just contact me.

have a good day,

Max

On Apr 17, 2015, at 2:18 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 4/17/15 2:02 PM, Ebert Maximilian wrote:
Hey List,

I already got a nice idea from Erik how to find residues bridged by a water
molecule by using the hbond tool and the map and index file. I still have a
question regarding the index. If I am not mistaken the first entry of bond
registry entry:

[ hbonds_Water-r_216_r_244 ] 4216   4217   3342 7225   7226   2962

should correspond to the last entry in the xpm file matrix:

/* y-axis:  0 1 2 3 4 5 6 7 8 9 10 11 12 */ " oo o  ooo oo  oo  ooo
ooo ooo o oo  o   o ooo ooo oo   oo o “,
"oo
“


and hence the last bond entry (7225   7226   2962) corresponds to the line
beneath the y-axis entry? Just to be sure. Is this correct? Couldn’t find any
hint what is described by Hydrogen Bond Index in the map file.


Yes, the .ndx and .xpm are "backwards" with respect to one another from the 
top-down perspective.  I wrote a script that does all the mapping if you want 
(parse_hbmap.pl) at 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html

It requires some modification of the .ndx file (you have to kill off all the 
lines that don't correspond to the actual hydrogen bonds) but it may save you 
some time to look through it.

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

==
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[gmx-users] g_hbond never shows hbond with HW2

[Ebert Maximilian]

Dear list,

I discovered something strange today. In my hbond search i find only HW1 of the 
water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to 
the fact that I am using SPC water? I can see the atom IDs of HW2 in the [ 
donors_hydrogens_Water ] entry in the ndx file. So technically GROMACs searched 
for HW2 donor connections but never finds any. However, thousands of hbonds are 
found with HW1.

Any thoughts on that? Thanks,

Max
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Re: [gmx-users] g_hbond never shows hbond with HW2

[Ebert Maximilian]

Thanks Justin. I just found out myself and wanted to answer my own question. 
But you are just too fast.

Have a good one,

Max

> On May 1, 2015, at 11:30 AM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/1/15 11:27 AM, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I discovered something strange today. In my hbond search i find only HW1 of 
>> the water forming a hydrogen bond as donor hydrogen and never HW2. Is this 
>> due to the fact that I am using SPC water? I can see the atom IDs of HW2 in 
>> the [ donors_hydrogens_Water ] entry in the ndx file. So technically GROMACs 
>> searched for HW2 donor connections but never finds any. However, thousands 
>> of hbonds are found with HW1.
>> 
>> Any thoughts on that? Thanks,
>> 
> 
> This is default behavior because of -merge.  If you want to differentiate 
> between different H on the same donor, use -nomerge.
> 
> -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] Ligand covalently bound to protein: Best practice

[Ebert Maximilian]

Hi there,

I am about to setup a protein ligand complex in which the the amino acid is 
covalently bound to the ligand. What I was about to do is to build an 
artificial amino acid (in this case serine) with the ligand attached to it an 
derive partial charges using antechamber or the RED server. Then while 
preparing the force field in GROMACS I would treat the serine was a new residue 
type with the new FF information. Is the a good practice? 

Thanks very much,

Max
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Re: [gmx-users] Ligand covalently bound to protein: Best practice

[Ebert Maximilian]

Thanks for your comment and sorry for my weird english. I must have been in my 
thoughts :).

I was also wondering if I attach covalently a protein to another protein or a 
large organic molecule through a residue in the middle of the sequence my 
approach would not work. Does anyone have a suggestion how setup a system like 
this?

Thanks,
Max


> On May 21, 2015, at 4:41 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/21/15 4:30 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am about to setup a protein ligand complex in which the the amino acid is 
>> covalently bound to the ligand. What I was about to do is to build an 
>> artificial amino acid (in this case serine) with the ligand attached to it 
>> an derive partial charges using antechamber or the RED server. Then while 
>> preparing the force field in GROMACS I would treat the serine was a new 
>> residue type with the new FF information. Is the a good practice?
>> 
> 
> Sounds reasonable.
> 
> -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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

Hi there,

I am about to setup a water:organic solvent mixture with a protein. I found 
many organic molecules on http://virtualchemistry.org with definitions for the 
OPLS FF. However, some are missing so I would need to derive the parameters 
myself. Before going into more details I was wondering if OPLS is to be 
preferred if organic solvent is present or can AMBER also be used? It seems 
that using ACPYPE with AMBER is much more accessible than using any other 
method to derive the parameters for organic molecules.

Thanks for your advice.
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Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

 density and 
see how it matches with reality.

What do you think about this approach? What would have been a better way? How 
can I make sure that the charges are correct?

Thanks for your input.

Max



On May 27, 2015, at 11:54 AM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:

Hi there,

I am about to setup a water:organic solvent mixture with a protein. I found 
many organic molecules on http://virtualchemistry.org with definitions for the 
OPLS FF. However, some are missing so I would need to derive the parameters 
myself. Before going into more details I was wondering if OPLS is to be 
preferred if organic solvent is present or can AMBER also be used? It seems 
that using ACPYPE with AMBER is much more accessible than using any other 
method to derive the parameters for organic molecules.

Thanks for your advice.
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Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with 
acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the 
virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value 
on their website) and for the parameter derived as explain in previous mail I 
got 817.0 which seems too high. Does anybody has an advice how I could improve 
the derivation of my parameters?

Thank you very much,

max

 
> On May 27, 2015, at 3:25 PM, Ebert Maximilian  wrote:
> 
> I read more about organic solvents in MD and came to the conclusion that OPLS 
> is indeed the best way to go. Since I couldn’t really find an accessible 
> tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will 
> document my progress here. Maybe this is of help for somebody in the future. 
> In addition, I would like to ask the community to help me in case you see 
> problems with my approach. Once I have a good protocol I will write a 
> tutorial and make it available online.
> 
> To validate my approach I am trying to create a parameter set for acetone 
> which I found on  http://virtualchemistry.org. To generate the OPLS topology 
> I used a tool suggested by many people called mktop in version 2.2.1. I 
> downloaded the ideal geometry of acetone from Ligand Expo and generated a 
> GROMACS topology file using the following command:
> 
> mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes
> 
> In order to get the charges for this organic molecule I downloaded the most 
> recent amber tools and compiled it. I used the AM1-BCC charge model to 
> generate charges for acetone using the following instructions in antechamber:
> 
> antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2
> 
> I opened the resulting mol2 file in Chimera to map the atoms to the atoms in 
> my .top file. The charges calculated by antechamber look reasonable and are 
> comparable to the validated OPLS topology from virtual chemistry:
> 
> virtual chemistry charges
> 
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
> chargeB  massB
> 1  opls_280 1   LIG C 1  0.47
> 12.011
> 2  opls_135 1   LIG C 2 -0.18
> 12.011
> 3  opls_135 1   LIG C 3 -0.18
> 12.011
> 4  opls_281 1   LIG O 4 -0.47   
> 15.9994
> 5  opls_282 1   LIG H 5  0.06 
> 1.008
> 6  opls_282 1   LIG H 6  0.06 
> 1.008
> 7  opls_282 1   LIG H 7  0.06 
> 1.008
> 8  opls_282 1   LIG H 8  0.06 
> 1.008
> 9  opls_282 1   LIG H 9  0.06 
> 1.008
>10  opls_282 1   LIG H10  0.06 
> 1.008
> 
> 
> antechamber AM1-BCC derived
> 
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
> chargeB  massB
>1  opls_280   1   ACN  C110.56 12.011
>2  opls_281   1   ACN  O11   -0.52 15.9994
>3  opls_135   1   ACN  C22   -0.20 12.011
>4  opls_135   1   ACN  C33   -0.20 12.011
>5  opls_282   1   ACN  H120.06 1.008
>6  opls_282   1   ACN  H220.06 1.008
>7  opls_282   1   ACN  H320.06 1.008
>8  opls_282   1   ACN  H430.06 1.008
>9  opls_282   1   ACN  H530.06 1.008
>   10  opls_282   1   ACN  H630.06 1.008
> 
> The atom types were guessed correctly by mktop and also the charge groups 
> make sense I think. So far so good.
> 
> I realize some differences between the two topologies. First the mktop 
> topology also includes FF constants for the different bonds and angles:
> 
> [ bonds ]
> 1 2 1   0.121  476976.0
> 1 3 1   0.151  265265.6
> 1 4 1   0.151  265265.6
> 3 5 1   0.109  284512.0
> 3 6 1   0.109  284512.0
> 3 7 1   0.109  284512.0
> 4 8 1   0.109  284512.0
> 4 9 1   0.109  284512.0
> 4 10 1   0.109  284512.0
> 
> 
> [ angles ]
> 1 3 5 1  109.460  292.880
> 1 3 6 1  109.473  292.880
> 1 3 7 1  109.484  292.880
> 1 4 8 1  109.466  292.880
> 1 4 9 1  109.435  292.880
> 1 4 10 1  109.477  292.880
> 2 1 3 1  119.985  669.440
> 2 1 4 1  119.985  669.440
> 3 1 4 1  120.029  585.760
> 5 3 6 1  109.445  276.144
> 5 3 7 1  109.464  276.144
> 6 3 7 1  109.502  276.144
> 8 4 9 1  109.483  276.14

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

Thanks Justin and Kalev this brings me already much further. I tried 
ffld_server and it works just fine. However, it is like a black box. I can’t 
really find the documentation on how ffld_server gets the charges. Do you know 
where to find the documentation?

Thanks

> On May 28, 2015, at 2:22 AM, Kalev Takkis  wrote:
> 
> If you're after OPLS topologies for GROMACS then one way to derive them is
> via Schrödinger's Maestro (free academics version is sufficient) and
> Andrey Frolov's
> ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
> create a force field represesentation of a molecule with the former
> (described here http://www.schrodinger.com/kb/809) and then convert it to
> GROMACS format with the latter.
> 
> All the best,
> Kalev
> 
> On 28 May 2015 at 03:37, Mohd Farid Ismail 
> wrote:
> 
>> You can try R.E.D. Server.  It has more charge models (I don't know
>> whether that will help).
>> 
>> Also, IMO, one should target the density and the static dielectric
>> constant when it comes to VDW and partial charges.  I saw a recent paper
>> that might be of interest to you
>> http://pubs.acs.org/doi/abs/10.1021/jp3002383
>> 
>> --
>> Mohd Farid Ismail
>> 
>> 
>> 
>> 
>> 28.05.2015, 05:13, "Ebert Maximilian" :
>> 
>> I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with
>> acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For
>> the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2
>> value on their website) and for the parameter derived as explain in
>> previous mail I got 817.0 which seems too high. Does anybody has an advice
>> how I could improve the derivation of my parameters?
>> 
>> Thank you very much,
>> 
>> max
>> 
>> On May 27, 2015, at 3:25 PM, Ebert Maximilian 
>> wrote:
>> 
>> I read more about organic solvents in MD and came to the conclusion that
>> OPLS is indeed the best way to go. Since I couldn’t really find an
>> accessible tutorial how to derive topology files for GROMACS and the FF
>> OPLS/AA I will document my progress here. Maybe this is of help for
>> somebody in the future. In addition, I would like to ask the community to
>> help me in case you see problems with my approach. Once I have a good
>> protocol I will write a tutorial and make it available online.
>> 
>> To validate my approach I am trying to create a parameter set for acetone
>> which I found on  http://virtualchemistry.org. To generate the OPLS
>> topology I used a tool suggested by many people called mktop in version
>> 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and
>> generated a GROMACS topology file using the following command:
>> 
>> mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes
>> 
>> In order to get the charges for this organic molecule I downloaded the
>> most recent amber tools and compiled it. I used the AM1-BCC charge model to
>> generate charges for acetone using the following instructions in
>> antechamber:
>> 
>> antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2
>> 
>> I opened the resulting mol2 file in Chimera to map the atoms to the atoms
>> in my .top file. The charges calculated by antechamber look reasonable and
>> are comparable to the validated OPLS topology from virtual chemistry:
>> 
>> virtual chemistry charges
>> 
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>> typeBchargeB  massB
>> 1  opls_280 1   LIG C 1  0.47
>>   12.011
>> 2  opls_135 1   LIG C 2 -0.18
>>   12.011
>> 3  opls_135 1   LIG C 3 -0.18
>>   12.011
>> 4  opls_281 1   LIG O 4 -0.47
>>  15.9994
>> 5  opls_282 1   LIG H 5  0.06
>>1.008
>> 6  opls_282 1   LIG H 6  0.06
>>1.008
>> 7  opls_282 1   LIG H 7  0.06
>>1.008
>> 8  opls_282 1   LIG H 8  0.06
>>1.008
>> 9  opls_282 1   LIG H 9  0.06
>>1.008
>>10  opls_282 1   LIG H10  0.06
>>1.008
>> 
>> 
>> antechamber AM1-BCC derived
>> 
>> [ atoms ]
>> ;   nr   

[gmx-users] Rule for atom names in GROMACS

[Ebert Maximilian]

Hi there,

While building my own topology I was wondering if the atom name is only used to 
link .gro atoms with .top entries. The behaviour of an atom is defined by the 
atom type and the atom name should not have any effect on the simulation right? 
So if I choose an atom name for a carbon as C, C11 or C2 the outcome should be 
the same as long as the atom has the same name in .gro and .top and the same 
type. Am I correct here? So atom names are used to link .top and .gro and later 
in visualization softwares like VMD to place a carbon atom in the GUI instead 
of something else. Correct?

Finally I was wondering if the atom name needs to be unique within a molecule.

Thanks for the clarification,

Max
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Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

I continued to define good partial charges using the tools suggested. I found 
that the combination of Maestro + ffconv or mktop, ACPYPE and antechamber + 
mktop have all advantages and disadvantages depending on the organic molecule. 

for instance for acetone with maestro and mktop i could achieve the same 
topology as virtual chemistry. I next tried to generate a topology for 
iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes 
density to the experimental one. I also tried to calculate the heat capacity 
with Cp and Cv to compare it with the literature. My box is 2.3x2.3x2.3nm large 
and has about 150 molecules of the organic solvent. After 1ns of NPT i get 
values which are 5x higher than the literature value (gmx energy -f npt.edr 
-fluct_props -nmol 100). I also tried a box 5x5x5nm with over 1000 molecules 
and got the same result. Any idea why the simulation using OPLS AA FF is so far 
of when it comes to the heat capacity?

thanks
max



> On May 28, 2015, at 9:19 AM, Ebert Maximilian  wrote:
> 
> Thanks Justin and Kalev this brings me already much further. I tried 
> ffld_server and it works just fine. However, it is like a black box. I can’t 
> really find the documentation on how ffld_server gets the charges. Do you 
> know where to find the documentation?
> 
> Thanks
> 
>> On May 28, 2015, at 2:22 AM, Kalev Takkis  wrote:
>> 
>> If you're after OPLS topologies for GROMACS then one way to derive them is
>> via Schrödinger's Maestro (free academics version is sufficient) and
>> Andrey Frolov's
>> ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
>> create a force field represesentation of a molecule with the former
>> (described here http://www.schrodinger.com/kb/809) and then convert it to
>> GROMACS format with the latter.
>> 
>> All the best,
>> Kalev
>> 
>> On 28 May 2015 at 03:37, Mohd Farid Ismail 
>> wrote:
>> 
>>> You can try R.E.D. Server.  It has more charge models (I don't know
>>> whether that will help).
>>> 
>>> Also, IMO, one should target the density and the static dielectric
>>> constant when it comes to VDW and partial charges.  I saw a recent paper
>>> that might be of interest to you
>>> http://pubs.acs.org/doi/abs/10.1021/jp3002383
>>> 
>>> --
>>> Mohd Farid Ismail
>>> 
>>> 
>>> 
>>> 
>>> 28.05.2015, 05:13, "Ebert Maximilian" :
>>> 
>>> I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with
>>> acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For
>>> the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2
>>> value on their website) and for the parameter derived as explain in
>>> previous mail I got 817.0 which seems too high. Does anybody has an advice
>>> how I could improve the derivation of my parameters?
>>> 
>>> Thank you very much,
>>> 
>>> max
>>> 
>>> On May 27, 2015, at 3:25 PM, Ebert Maximilian 
>>> wrote:
>>> 
>>> I read more about organic solvents in MD and came to the conclusion that
>>> OPLS is indeed the best way to go. Since I couldn’t really find an
>>> accessible tutorial how to derive topology files for GROMACS and the FF
>>> OPLS/AA I will document my progress here. Maybe this is of help for
>>> somebody in the future. In addition, I would like to ask the community to
>>> help me in case you see problems with my approach. Once I have a good
>>> protocol I will write a tutorial and make it available online.
>>> 
>>> To validate my approach I am trying to create a parameter set for acetone
>>> which I found on  http://virtualchemistry.org. To generate the OPLS
>>> topology I used a tool suggested by many people called mktop in version
>>> 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and
>>> generated a GROMACS topology file using the following command:
>>> 
>>> mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes
>>> 
>>> In order to get the charges for this organic molecule I downloaded the
>>> most recent amber tools and compiled it. I used the AM1-BCC charge model to
>>> generate charges for acetone using the following instructions in
>>> antechamber:
>>> 
>>> antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2
>>> 
>>> I opened the resulting mol2 file in Chimera to map the atoms to the atoms
>>> in my .top file. The charges calculated by antecham

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

[Ebert Maximilian]

Hi Dewey,

maybe a little bit off topic but your description of the system reminded me of 
a paper I read a couple of years ago. Do you know about the ABF method and the 
work of Lamoureux et al? (http://pubs.acs.org/doi/abs/10.1021/ja300129x) maybe 
worth checking because it sounds like the simulation you want to execute (even 
though they don’t use GROMACS).

Max

On May 31, 2015, at 4:17 PM, MPI mailto:mpi...@gmail.com>> 
wrote:

Dear Users,

   I have a protein-lipid bilayer system and this protein is an ion
channel.  I would like to force a substrate eg, ammonia (NH3) passing
through this channel.

I wonder when it is appropriate to add NH3 into the system and how to
setup the control of temperature coupling in thermostats.
For example,

1.  add NH3 first with the protein and  then embed protein-NH3  into the lipid

or

2.  embed the protein into  lipid with an equilibration,  followed by
adding NH3 into the system


Also,  if the substrate has a charge, which order is preferred ?


Thanks,
Dewey
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Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

Hi,

thanks diana for your input and for the review. I never used GROMOS so far and 
I feel less comfortable using an unknown FF at this point. I am writing a 
tutorial on how to parameterize organic molecules right now and will publish it 
this week. Maybe you can comment on the strategy to have a relatively clean and 
broad approach. I was wondering which physical-chemical properties did you use 
to verify your definition? So far I am looking at density, Cp and Cv.

Thanks!

Max

> On May 28, 2015, at 5:15 AM, Diana Lousa  wrote:
> 
> Hi,
> 
> Our group has done many studies using enzymes in organic solvents (with
> different amounts of water) and we always used the GROMOS FF for the
> proteins and compatible  parameters for the solvents. We can find a review
> of enzyme simulations in nonaqueous solvents here:
> http://pubs.rsc.org/en/Content/ArticleLanding/2013/CP/c3cp51761f#!divAbstract
> 
> 
> The parameters that we used for different solvents were able to reproduce
> their physical-chemical properties. I can also tell you that from our
> experience the latest GROMOS FF are able to reproduce the structural
> properties of small peptides and proteins also seem to be quite stable when
> these FF are used. Thus, using GROMOS 54A7 for the protein and compatible
> parameters for organic solvents can be a good choice. However, if you want
> to use PME for long-range electrostatics, you have to test if these
> parameters work in these conditions, because they were developed to be used
> with RF.
> 
> 
> On Thu, May 28, 2015 at 7:22 AM, Kalev Takkis 
> wrote:
> 
>> If you're after OPLS topologies for GROMACS then one way to derive them is
>> via Schrödinger's Maestro (free academics version is sufficient) and
>> Andrey Frolov's
>> ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
>> create a force field represesentation of a molecule with the former
>> (described here http://www.schrodinger.com/kb/809) and then convert it to
>> GROMACS format with the latter.
>> 
>> All the best,
>> Kalev
>> 
>> On 28 May 2015 at 03:37, Mohd Farid Ismail 
>> wrote:
>> 
>>> You can try R.E.D. Server.  It has more charge models (I don't know
>>> whether that will help).
>>> 
>>> Also, IMO, one should target the density and the static dielectric
>>> constant when it comes to VDW and partial charges.  I saw a recent paper
>>> that might be of interest to you
>>> http://pubs.acs.org/doi/abs/10.1021/jp3002383
>>> 
>>> --
>>> Mohd Farid Ismail
>>> 
>>> 
>>> 
>>> 
>>> 28.05.2015, 05:13, "Ebert Maximilian" :
>>> 
>>> I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled
>> with
>>> acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3.
>> For
>>> the virtual chemistry parameters i calculated 798.6 (close to the
>> 800.1±0.2
>>> value on their website) and for the parameter derived as explain in
>>> previous mail I got 817.0 which seems too high. Does anybody has an
>> advice
>>> how I could improve the derivation of my parameters?
>>> 
>>> Thank you very much,
>>> 
>>> max
>>> 
>>> On May 27, 2015, at 3:25 PM, Ebert Maximilian 
>>> wrote:
>>> 
>>> I read more about organic solvents in MD and came to the conclusion that
>>> OPLS is indeed the best way to go. Since I couldn’t really find an
>>> accessible tutorial how to derive topology files for GROMACS and the FF
>>> OPLS/AA I will document my progress here. Maybe this is of help for
>>> somebody in the future. In addition, I would like to ask the community to
>>> help me in case you see problems with my approach. Once I have a good
>>> protocol I will write a tutorial and make it available online.
>>> 
>>> To validate my approach I am trying to create a parameter set for
>> acetone
>>> which I found on  http://virtualchemistry.org. To generate the OPLS
>>> topology I used a tool suggested by many people called mktop in version
>>> 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and
>>> generated a GROMACS topology file using the following command:
>>> 
>>> mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect
>> yes
>>> 
>>> In order to get the charges for this organic molecule I downloaded the
>>> most recent amber tools and compiled it. I used the AM1-BCC charge model
>> to
>>> generate charges for acetone using the following 

Re: [gmx-users] trjcat issue

[Ebert Maximilian]

Hi,

try to set the time manually. It fixed the problem for me (-settime).

Max

> On May 28, 2015, at 4:43 AM, Giannis Gl  wrote:
> 
> Dear all,
> 
> I tried to concatenate two trajectories using the comand
> trjcat -f Trajectory_total.xtc md26_out.xtc -o Trajectory_total_full.xtc
> 
> The process ended normaly:
> 
> Reading frame   1 time 3000310.000
> 
> Summary of files and start times used:
> 
>  FileStart time   Time step
> -
> Trajectory_total.xtc0.000 ps   10.000 ps
> md26_out.xtc   3000300.000 ps   10.000 ps
> 
> Reading frame   0 time0.000
> 
> Continue writing frames from Trajectory_total.xtc t=0 ps, frame=0
> Reading frame  314000 time 314.000->  frame 30 time 300.000
> ps
> Reading frame   0 time 3000300.000
> lasttime 3.00029e+06
> 
> Continue writing frames from md26_out.xtc t=3.0003e+06 ps,
> frame=300030
> ->  frame 314720 time 3147200.000 ps ->  frame 314030 time 3140300.000
> ps
> 
> Last frame written was 314720, time 3147200.00 ps
> 
> 
> But when I tried to see any frame after 3300.000 ps
> I ended up with an error like
> Fatal error:
> Specified frame (time 30003000.00) doesn't exist or file
> corrupt/inconsistent.
> 
> What have I done wrong?
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Re: [gmx-users] Volume of active site

[Ebert Maximilian]

Hi Raja,

you could also give 3V a try: http://3vee.molmovdb.org

Cheers,
Max

On Jun 1, 2015, at 11:12 AM, Erik Marklund 
mailto:erik.markl...@chem.ox.ac.uk>> wrote:

Dear Raja,

Depending on how you define that volume, you may achieve what you want through 
clever use of g_sas -tv (gmx sas nowadays).

Kind regards,
Erik

On 1 Jun 2015, at 15:19, Raj D 
mailto:gromacs.fo...@gmail.com>> wrote:

Dear user,
I have completed a set of MD simulations of mutants and wild type of a
protein complexed with its substrate in its active site , I have inferred
that the active sites of all mutant enzymes have gone enlarged relative to
wild type which is  consistent with our kinetic study of the mutants, the
Km values are so high for all mutant enzymes and I would like quantify the
volume of the active site comprising a set of 17 active site residues ..Is
there any direct or indirect tool in gromacs to compute the volume like
that ? Or any free tools available .
Regards,
Raja
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Re: [gmx-users] VMD Visulazation

[Ebert Maximilian]

Hey Victor,

check http://manual.gromacs.org/current/programs/gmx-trjconv.html you probably 
need -ur and -pbc

Cheers,

Max

On Jun 1, 2015, at 1:45 PM, Victor Ma 
mailto:victordsmag...@gmail.com>> wrote:

Hello Justin,

Thanks a lot for the quick response. So I first load the .gro file from the
previous step which is my initial coordinate file, I then loaded the .trr
file. But I am getting some wired image. Please see attachment. Thank you.

Victor
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Re: [gmx-users] Looking for FF parameters for bivalent metals and oxoguanine

[Ebert Maximilian]

Hi Timofey,

did you check http://ambermd.org/tutorials/basic/tutorial4b/ or 
https://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs

cheers,

Max

On Jun 3, 2015, at 12:24 AM, Timofey Tyugashev 
mailto:tyugas...@niboch.nsc.ru>> wrote:

I'm investigating several protein-DNA systems with AMBER 99SB force field . 
Some of them involve 8-oxoG lesions and metal-dependent enzymes.
Is there any reliable calculated parameters for them or any reliable and 
reasonably quick way to derive them?
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[gmx-users] Questions about the topology file format

[Ebert Maximilian]

Hi there,

I have two quick questions about the topology file format which I couldn’t find 
in the documentary. The semi-colon is giving me some headache. Is it always a 
comment which is written after?

First:

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
 1 opls_135 1   IPAC11-0.111600 12.01100 ; qtot -0.112  
CT 

is qtot and CT used for anything and is it interpreted since it is after the ;

Second:

[ bonds ]
;   ai aj funct   r k
 1  2   1 ;1.5350e-012.5363e+05 ; C1 - C2 CT - CT   
 

are the values for r and k here used since they are after the ; and what is 
C1-C2 and CT-CT used for and why another ;?

Thank you very much for clarification.

Max

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Re: [gmx-users] error group protein not found

[Ebert Maximilian]

Hi,

if there is a protein in your system you should have protein as standard group. 
Maybe you use a template mdp file in which the temperature coupling group is 
protein. if you have no protein in your simulation check the mdp files for 
tc-grps and adjust accordingly.

Max



> On Jun 3, 2015, at 3:07 PM, Victor Rosas Garcia  
> wrote:
> 
> Hello,
> 
> In your command line you do not specify an index file. Maybe you need to
> generate one.  Check out usage of make_ndx.
> 
> Hope this helps
> 
> Victor
> 
> 2015-06-03 13:41 GMT-05:00 marzieh dehghan :
> 
>> Hi every body
>> 
>> I create a covalent bond and now I want to held MD by gromacs,
>> 
>> after holding the following command : grompp -f nvt.mdp -c em.gro -p
>> topol.top -o nvt.tpr
>> 
>> I confornted to an error:
>> 
>> Fatal error:
>> Group Protein not found in index file.
>> Group names must match either [moleculetype] names
>> or custom index group names,in which case you
>> must supply an index file to the '-n' option of grompp.
>> 
>> 
>> please let me know how can I solve this problem.
>> 
>> I am looking forward to getting your answer
>> 
>> thanks a lot
>> 
>> 
>> --
>> 
>> 
>> 
>> 
>> *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
>> Biophysics (IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Ebert Maximilian]

I just finished to write a tutorial on how to parameterize an organic molecule 
in OPLS/AA using MKTop, TopolGen, ACPYPE, RED Server, antechamber and 
Schrodinger Maestro. I also added a part to valid the charges and the final 
topology. Any comments, corrections and improvements are more than welcome.

http://www.esi.umontreal.ca/~pelletjo/gromacs/derive01.html

I reference Justin’s tutorials a lot. Thanks again to you for taking so much 
time and share them with the community. You make GROMACS so much more 
accessible for new users.

Max

On May 29, 2015, at 2:53 PM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:

I continued to define good partial charges using the tools suggested. I found 
that the combination of Maestro + ffconv or mktop, ACPYPE and antechamber + 
mktop have all advantages and disadvantages depending on the organic molecule.

for instance for acetone with maestro and mktop i could achieve the same 
topology as virtual chemistry. I next tried to generate a topology for 
iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes 
density to the experimental one. I also tried to calculate the heat capacity 
with Cp and Cv to compare it with the literature. My box is 2.3x2.3x2.3nm large 
and has about 150 molecules of the organic solvent. After 1ns of NPT i get 
values which are 5x higher than the literature value (gmx energy -f npt.edr 
-fluct_props -nmol 100). I also tried a box 5x5x5nm with over 1000 molecules 
and got the same result. Any idea why the simulation using OPLS AA FF is so far 
of when it comes to the heat capacity?

thanks
max



On May 28, 2015, at 9:19 AM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:

Thanks Justin and Kalev this brings me already much further. I tried 
ffld_server and it works just fine. However, it is like a black box. I can’t 
really find the documentation on how ffld_server gets the charges. Do you know 
where to find the documentation?

Thanks

On May 28, 2015, at 2:22 AM, Kalev Takkis 
mailto:kalev.tak...@gmail.com>> wrote:

If you're after OPLS topologies for GROMACS then one way to derive them is
via Schrödinger's Maestro (free academics version is sufficient) and
Andrey Frolov's
ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
create a force field represesentation of a molecule with the former
(described here http://www.schrodinger.com/kb/809) and then convert it to
GROMACS format with the latter.

All the best,
Kalev

On 28 May 2015 at 03:37, Mohd Farid Ismail 
mailto:mohd.farid.ism...@yandex.com>>
wrote:

You can try R.E.D. Server.  It has more charge models (I don't know
whether that will help).

Also, IMO, one should target the density and the static dielectric
constant when it comes to VDW and partial charges.  I saw a recent paper
that might be of interest to you
http://pubs.acs.org/doi/abs/10.1021/jp3002383

--
Mohd Farid Ismail




28.05.2015, 05:13, "Ebert Maximilian" :

I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with
acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For
the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2
value on their website) and for the parameter derived as explain in
previous mail I got 817.0 which seems too high. Does anybody has an advice
how I could improve the derivation of my parameters?

Thank you very much,

max

On May 27, 2015, at 3:25 PM, Ebert Maximilian 
wrote:

I read more about organic solvents in MD and came to the conclusion that
OPLS is indeed the best way to go. Since I couldn’t really find an
accessible tutorial how to derive topology files for GROMACS and the FF
OPLS/AA I will document my progress here. Maybe this is of help for
somebody in the future. In addition, I would like to ask the community to
help me in case you see problems with my approach. Once I have a good
protocol I will write a tutorial and make it available online.

To validate my approach I am trying to create a parameter set for acetone
which I found on  http://virtualchemistry.org. To generate the OPLS
topology I used a tool suggested by many people called mktop in version
2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and
generated a GROMACS topology file using the following command:

mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes

In order to get the charges for this organic molecule I downloaded the
most recent amber tools and compiled it. I used the AM1-BCC charge model to
generate charges for acetone using the following instructions in
antechamber:

antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2

I opened the resulting mol2 file in Chimera to map the atoms to the atoms
in my .top file. The charges calculated by antechamber look reasonable and
are comparable to the validated OPLS topology from virtual chemistry:

virtual chemistry charges

[ atoms ]
;   nr   type  

Re: [gmx-users] Is gromacs tutorial website down?

[Ebert Maximilian]

The website is down but available in the google cache. Justin said he is 
working on bringing it back.

Max

> On Jun 4, 2015, at 3:49 PM, 朱文鹏  wrote:
> 
> Hello,
> 
> I cannot open the gromacs tutorial website (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/).
> 
> Do you have the same problems?
> 
> Best,
> -Jason
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[gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

Dear list,

I ran into some problem to define the topology of phenyl palmitate. My main 
problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of 
the molecule without hydrogen (I hope it turns out to be readable in the email):


  O17
   ||
C21 - C20 C16 (C)n
   /\   / \  /   \
C22  C19 - O18  C15C1
   \/
C23 - C24

I think I defined the atom types correctly:

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   
 1 opls_768 1   PNR   C224-0.1952 12.01100  
 2 opls_145 1   PNR   C215-0.0500 12.01100  
 3 opls_145 1   PNR   C206-0.1550 12.01100 
 4 opls_145 1   PNR   C237-0.0500 12.01100   
 5 opls_145 1   PNR   C248-0.1550 12.01100   
 6 opls_472 1   PNR   C199 0.1591 12.01100 
 7 opls_473 1   PNR   O18   10-0.3732 15.99940   
 8 opls_465 1   PNR   C16   11 0.6491 12.01100
 9 opls_466 1   PNR   O17   12-0.5100 15.99940   
10 opls_136 1   PNR   C15   13-0.1264 12.01100 
11 opls_136 1   PNR   C14   14-0.0804 12.01100
12 ….

The problem is now in the ester since there is no dihedral definition of CA OS 
C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is 
Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I 
understand 472 correctly? How can I resolve the missing two dihedral angles? 

I also wanted to know if somebody has an idea what is meant by: AA C:   esters 
- for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case 
to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since 
they are the R of the ester?

Thank you very much for your advice,

Max





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Re: [gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

Hi,

a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined 
OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT 
in OPLS/AA. Any thoughts on that? I really have difficulties to visualize 
dihedral angles and I am not sure if this would actually give roughly the same 
geometry or not.

Thanks and have a good weekend.

Max

> On Jun 5, 2015, at 4:38 PM, Ebert Maximilian  wrote:
> 
> Dear list,
> 
> I ran into some problem to define the topology of phenyl palmitate. My main 
> problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch 
> of the molecule without hydrogen (I hope it turns out to be readable in the 
> email):
> 
> 
>  O17
>   ||
>C21 - C20 C16 (C)n
>   /\   / \  /   \
> C22  C19 - O18  C15C1
>   \/
>C23 - C24
> 
> I think I defined the atom types correctly:
> 
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr charge  mass   
> 1 opls_768 1   PNR   C224-0.1952 12.01100  
> 2 opls_145 1   PNR   C215-0.0500 12.01100  
> 3 opls_145 1   PNR   C206-0.1550 12.01100 
> 4 opls_145 1   PNR   C237-0.0500 12.01100   
> 5 opls_145 1   PNR   C248-0.1550 12.01100   
> 6 opls_472 1   PNR   C199 0.1591 12.01100 
> 7 opls_473 1   PNR   O18   10-0.3732 15.99940   
> 8 opls_465 1   PNR   C16   11 0.6491 12.01100
> 9 opls_466 1   PNR   O17   12-0.5100 15.99940   
>10 opls_136 1   PNR   C15   13-0.1264 12.01100 
>11 opls_136 1   PNR   C14   14-0.0804 12.01100
>12 ….
> 
> The problem is now in the ester since there is no dihedral definition of CA 
> OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 
> which is Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl 
> ester). Do I understand 472 correctly? How can I resolve the missing two 
> dihedral angles? 
> 
> I also wanted to know if somebody has an idea what is meant by: AA C:   
> esters - for R on C=O, use #280-#282 of the atom type opls_465. Do I need in 
> this case to assign opls_280 to C15 and opls_282 to the corresponding 
> hydrogens since they are the R of the ester?
> 
> Thank you very much for your advice,
> 
> Max
> 
> 
> 
> 
> 
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Re: [gmx-users] Pressure Coupling in GROMACS

[Ebert Maximilian]

Hi Ashraf,

from the gromacs website 
(http://www.gromacs.org/Documentation/Terminology/Berendsen):

The distribution of temperatures and pressures (in the case of the thermostat 
and barostat, respectively) does not correspond to any known statistical 
mechanical ensemble.  It is best applied during the early stages of 
equilibration, as it converges relatively quickly and can be useful for 
stabilizing systems that may be far from equilibrium.

So you should ne use Berendsen for production only for equilibration. Check out 
one of those:

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

Max

On Jun 8, 2015, at 9:10 AM, Jashimuddin Ashraf 
mailto:jashimuddin.ashra...@gmail.com>> wrote:

Dear GROMACS users,

I am new to GROMACS. My system contains only carbon nanotubes and inside my
md.mdp file I have-


.
.
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 1; @pressure coupling 1ps
compressibility  = 4.5e-5;
ref_p= 1.0; @reference pressure
.
.



whenever I run the grompp command, I get a warning called-




Using Berendsen pressure coupling invalidates the true ensemble for the
thermostat


I looked up at the mail list where I found Parrinello-Rahman to be
appropriate for the NPT simulations. But I intend to run production MD. Is
this an error to be
worried about? (I can obviously run simulations using maxwarn)

I have another problem. When I simulated carbon nanotubes with water/ other
molecules, the average pressure I observed from simulation (using g_energy
command) had a good agreement with the ref_p. But now the average pressure
becomes independent of my ref_p. This is a problem that is bugging me for a
long time. How can I resolve this?

Thanks in advance.
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Re: [gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

Thanks for your response. First of all I must say it is a bit strange that OPLS 
has the atom types of phenyl ester but not the corresponding dihedral angels to 
support it. But I see your point but could you elaborate on how I could 
evaluate this? How can I calculate those profiles?

Thanks,

Max
On Jun 7, 2015, at 9:49 AM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 6/5/15 6:08 PM, Ebert Maximilian wrote:
Hi,

a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined 
OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT 
in OPLS/AA. Any thoughts on that? I really have difficulties to visualize 
dihedral angles and I am not sure if this would actually give roughly the same 
geometry or not.


The determining factor is whether or not the QM and MM energy profiles match as 
those dihedrals are rotated.

-Justin

Thanks and have a good weekend.

Max

On Jun 5, 2015, at 4:38 PM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:

Dear list,

I ran into some problem to define the topology of phenyl palmitate. My main 
problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of 
the molecule without hydrogen (I hope it turns out to be readable in the email):


 O17
  ||
   C21 - C20 C16 (C)n
  /\   / \  /   \
C22  C19 - O18  C15C1
  \/
   C23 - C24

I think I defined the atom types correctly:

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass
1 opls_768 1   PNR   C224-0.1952 12.01100
2 opls_145 1   PNR   C215-0.0500 12.01100
3 opls_145 1   PNR   C206-0.1550 12.01100
4 opls_145 1   PNR   C237-0.0500 12.01100
5 opls_145 1   PNR   C248-0.1550 12.01100
6 opls_472 1   PNR   C199 0.1591 12.01100
7 opls_473 1   PNR   O18   10-0.3732 15.99940
8 opls_465 1   PNR   C16   11 0.6491 12.01100
9 opls_466 1   PNR   O17   12-0.5100 15.99940
   10 opls_136 1   PNR   C15   13-0.1264 12.01100
   11 opls_136 1   PNR   C14   14-0.0804 12.01100
   12 ….

The problem is now in the ester since there is no dihedral definition of CA OS 
C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is 
Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I 
understand 472 correctly? How can I resolve the missing two dihedral angles?

I also wanted to know if somebody has an idea what is meant by: AA C:   esters 
- for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case 
to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since 
they are the R of the ester?

Thank you very much for your advice,

Max





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--
==

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

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

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

==
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Re: [gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

Maybe this is of interest to others so I will write what I did. I built a 
phenyl acetate and methyl acetate:

 O_2
   ||
  CA - CA C_2
 /  \   / \
CACA - OSCT
 \  /
  CA - CA


 O_2
   ||
 C_2
 / \
CT - OSCT


And I did a conformation search of the two molecules using QM/MM. After finding 
the best ideal gas solution I looked at the dihedral energy profile of CT OS 
C_2 O_2, CT OS C_2 CT, CA OS C_2 O_2 and CA OS C_2 CT. The pairs basically 
matched with the same energy minimum at the same angle. So I presume now that 
with a small error the approximation can be used. Of course I am not an expert 
as you can tell so if you have any additional thoughts please let me know.

Max


On Jun 8, 2015, at 9:35 AM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:

Thanks for your response. First of all I must say it is a bit strange that OPLS 
has the atom types of phenyl ester but not the corresponding dihedral angels to 
support it. But I see your point but could you elaborate on how I could 
evaluate this? How can I calculate those profiles?

Thanks,

Max
On Jun 7, 2015, at 9:49 AM, Justin Lemkul 
mailto:jalem...@vt.edu><mailto:jalem...@vt.edu>> wrote:



On 6/5/15 6:08 PM, Ebert Maximilian wrote:
Hi,

a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined 
OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT 
in OPLS/AA. Any thoughts on that? I really have difficulties to visualize 
dihedral angles and I am not sure if this would actually give roughly the same 
geometry or not.


The determining factor is whether or not the QM and MM energy profiles match as 
those dihedrals are rotated.

-Justin

Thanks and have a good weekend.

Max

On Jun 5, 2015, at 4:38 PM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca><mailto:m.eb...@umontreal.ca>>
 wrote:

Dear list,

I ran into some problem to define the topology of phenyl palmitate. My main 
problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of 
the molecule without hydrogen (I hope it turns out to be readable in the email):


O17
 ||
  C21 - C20 C16 (C)n
 /\   / \  /   \
C22  C19 - O18  C15C1
 \/
  C23 - C24

I think I defined the atom types correctly:

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass
   1 opls_768 1   PNR   C224-0.1952 12.01100
   2 opls_145 1   PNR   C215-0.0500 12.01100
   3 opls_145 1   PNR   C206-0.1550 12.01100
   4 opls_145 1   PNR   C237-0.0500 12.01100
   5 opls_145 1   PNR   C248-0.1550 12.01100
   6 opls_472 1   PNR   C199 0.1591 12.01100
   7 opls_473 1   PNR   O18   10-0.3732 15.99940
   8 opls_465 1   PNR   C16   11 0.6491 12.01100
   9 opls_466 1   PNR   O17   12-0.5100 15.99940
  10 opls_136 1   PNR   C15   13-0.1264 12.01100
  11 opls_136 1   PNR   C14   14-0.0804 12.01100
  12 ….

The problem is now in the ester since there is no dihedral definition of CA OS 
C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is 
Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I 
understand 472 correctly? How can I resolve the missing two dihedral angles?

I also wanted to know if somebody has an idea what is meant by: AA C:   esters 
- for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case 
to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since 
they are the R of the ester?

Thank you very much for your advice,

Max





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==

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

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

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[gmx-users] Cross-correlation map of protein residues

[Ebert Maximilian]

Dear list,

I am looking for a gromacs tool which is able to calculate/draw a map of 
residues which are either in their motion correlated or anti correlated. first 
i thought i could just use g_covar with c-alpha and use the -xpma option but 
while reading previous mailing list posts people said that the atomic 
covariance matrix does not correlate motions. All posts I found where older and 
the script from the gromacs site for a g_covar tool which can calculate the 
correlation plot is from 2009. Therefore, i wanted to know if gromacs 5 is able 
to directly calculate the plot. if not does anybody know a straight forward way 
of doing so for a gromacs trajectory?

thank you very much,

max
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Re: [gmx-users] Cross-correlation map of protein residues

[Ebert Maximilian]

Thanks for your reply. I saw it and tried to change the code to work with 
gromacs 5 but my output plot doesn’t seem right. the code is written for 
gromacs 3.3 and is not easily build agains 5. do you have a version working on 
5?

thanks

> On Jul 18, 2015, at 1:32 AM, bipin singh  wrote:
> 
> There is a modified version of g_covar available at the below link for
> calculating correlation matrix:
> 
> http://www.gromacs.org/Downloads/User_contributions/Other_software
> 
> http://www.gromacs.org/@api/deki/files/55/=g_covar.tgz
> 
> 
> --
> Thanks and Regards,
> Bipin Singh
> 
> On Fri, Jul 17, 2015 at 6:51 PM, Ebert Maximilian 
> wrote:
> 
>> Dear list,
>> 
>> I am looking for a gromacs tool which is able to calculate/draw a map of
>> residues which are either in their motion correlated or anti correlated.
>> first i thought i could just use g_covar with c-alpha and use the -xpma
>> option but while reading previous mailing list posts people said that the
>> atomic covariance matrix does not correlate motions. All posts I found
>> where older and the script from the gromacs site for a g_covar tool which
>> can calculate the correlation plot is from 2009. Therefore, i wanted to
>> know if gromacs 5 is able to directly calculate the plot. if not does
>> anybody know a straight forward way of doing so for a gromacs trajectory?
>> 
>> thank you very much,
>> 
>> max
>> --
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Re: [gmx-users] Create file topology in oplsaa

[Ebert Maximilian]

you can also look at this tutorial if you want to have starting point for 
generating topologies:

http://www.esi.umontreal.ca/~pelletjo/gromacs/

max

On Jul 21, 2015, at 9:52 AM, gozde ergin 
mailto:gozdeeer...@gmail.com>> wrote:

Gromacs has OPLSAA force field. You can use pdb2gmx command.

Also you can use topolbuild software. If you google it, you can easily find
how to use it.

On Tue, Jul 21, 2015 at 2:38 PM, Daniele Veclani 
mailto:danielevecl...@gmail.com>>
wrote:

Dear users

I'm trying to create a topology file  for a molecule to oplsaa force fields

How can I do this?

I have read that I can do this with the program MKTOP but I can not use it.

Is there a tutorial for this program?

Best regards
Daniele.
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[gmx-users] OPLS/AA parameters for 2-propanol

[Ebert Maximilian]

Dear list,

I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA 
format. Before deriving my own I thought it would be best to ask first. I saw 
some posts that people used 2-propanol in OPLS but couldn’t find any reference 
in google scholar. 

Thank you very much,

Max
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Re: [gmx-users] OPLS/AA parameters for 2-propanol

[Ebert Maximilian]

I saw the papers you mentioned but one is a not clear how they parameterized, 
one is missing the supporting material and the last is not showing the 
parameters they used. I will check with the initial paper of Jorgensen again 
but if I recall it correctly he mentioned some problems with iso-propanol. 

strange that such a common organic solvent is not easily accessible for OPLS.

thanks for your help johnny!

Max

> On Sep 1, 2015, at 11:41 PM, Johnny Lu  wrote:
> 
> that was by google. I haven't parametrized forcefields.
> did they just put the pieces in
> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
> for 2-propanol?
> 
> 
> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu  wrote:
> 
>> Not sure if those are for 2-propanol as a liquid or interaction between
>> 2-propanol and protein.
>> from googling "2 propanol opls/aa"
>> 
>> 1. Development and Testing of the OPLS All-Atom Force Field on
>> Conformational Energetics and Properties of Organic Liquids
>>  The parameters are in the supporting info.
>>  Seems not exactly 2-propanol. But it has parameter for organic
>> liquids.
>>  "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
>>  http://pubs.acs.org/doi/abs/10.1021/ja9621760
>> 
>> 2. A statistical model of hydrogen bond networks in liquid alcohols
>> 
>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf
>> 
>> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
>> of Macrocyclic Polyketides
>>  https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf
>> 
>> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian 
>> wrote:
>> 
>>> Dear list,
>>> 
>>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
>>> format. Before deriving my own I thought it would be best to ask first. I
>>> saw some posts that people used 2-propanol in OPLS but couldn’t find any
>>> reference in google scholar.
>>> 
>>> Thank you very much,
>>> 
>>> Max
>>> --
>>> 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] OPLS/AA parameters for 2-propanol

[Ebert Maximilian]

Thanks for the reply. I think I found relatively good atom types for iso 
propanol and derived the partial charges using antechamber and red server. I 
next check the density of pure iso propanol and used the closest definition to 
the real value. Iso propanol is used as co-solvent with water with a water:iso 
propanol ration of 90:10. I will just use my derived parameters then. 

Thanks for your replies. 

Max

> On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban  wrote:
> 
> Normally, this sort of things is done via mechanical combining of the
> known groups --  CH3, -CH, OH -- from the force field.
> 
> If your goal is to increase accuracy for pure 2-propanol per se, then
> play with the distribution of electronic density between OH and CH.
> 
> If 2-propanol is to be used as a solvent for somwthing else, this does
> ultimately not pay off.
> 
> 
> 
> 
> 
> 
> 
> 
>> On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian  
>> wrote:
>> I saw the papers you mentioned but one is a not clear how they 
>> parameterized, one is missing the supporting material and the last is not 
>> showing the parameters they used. I will check with the initial paper of 
>> Jorgensen again but if I recall it correctly he mentioned some problems with 
>> iso-propanol.
>> 
>> strange that such a common organic solvent is not easily accessible for OPLS.
>> 
>> thanks for your help johnny!
>> 
>> Max
>> 
>>> On Sep 1, 2015, at 11:41 PM, Johnny Lu  wrote:
>>> 
>>> that was by google. I haven't parametrized forcefields.
>>> did they just put the pieces in
>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
>>> for 2-propanol?
>>> 
>>> 
>>>> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu  wrote:
>>>> 
>>>> Not sure if those are for 2-propanol as a liquid or interaction between
>>>> 2-propanol and protein.
>>>> from googling "2 propanol opls/aa"
>>>> 
>>>> 1. Development and Testing of the OPLS All-Atom Force Field on
>>>> Conformational Energetics and Properties of Organic Liquids
>>>> The parameters are in the supporting info.
>>>> Seems not exactly 2-propanol. But it has parameter for organic
>>>> liquids.
>>>> "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
>>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760
>>>> 
>>>> 2. A statistical model of hydrogen bond networks in liquid alcohols
>>>> 
>>>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf
>>>> 
>>>> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
>>>> of Macrocyclic Polyketides
>>>> https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf
>>>> 
>>>> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian 
>>>> wrote:
>>>> 
>>>>> Dear list,
>>>>> 
>>>>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
>>>>> format. Before deriving my own I thought it would be best to ask first. I
>>>>> saw some posts that people used 2-propanol in OPLS but couldn’t find any
>>>>> reference in google scholar.
>>>>> 
>>>>> Thank you very much,
>>>>> 
>>>>> Max
>>>>> --
>>>>> Gromacs Users mailing list
>>>>> 
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>> 
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>>>>> 
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>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>> 
>>>> 
>>>> 
>>> --
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>>> 
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>> 
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>> 
>> * Please search the arc

Re: [gmx-users] OPLS/AA parameters for 2-propanol

[Ebert Maximilian]

Thanks for the answer again. So I saw that for self-diffusion and viscosity I 
can just use gmx tcaf and gmx msd. As an experimental setup, would a squared 
box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good 
system to use tcaf and msd?

For the heat of vaporization I saw that I could calculate DHvap =  - 
 + RT 

  is just Epot of the same MD I described above but for  I need a 
new calculation. If I understood it correctly I would need a box with the same 
number of molecules as in the previous calculation but separate them with a lot 
of space (50nm was suggested). In addition, turn off PBC, PME, L-J and coulomb 
cut-offs. Get Epot from this calculation and use the formular. 

Would these approaches be correct?

Thank you very much. 

Max

> On Sep 2, 2015, at 5:02 PM, Vitaly V. Chaban  wrote:
> 
> It is difficult to get a very wrong density, especially for relatively
> rigid compounds. In the meantime, deviations of density within 2% of
> the experimental value should be admitted acceptable.
> 
> A better criterion is to compare self-diffusion or viscosity to the
> experiment. Another famous property for parametrization is heat of
> vaporization.
> 
> 
> 
> 
> 
> 
> On Wed, Sep 2, 2015 at 3:22 PM, Ebert Maximilian  wrote:
>> Thanks for the reply. I think I found relatively good atom types for iso 
>> propanol and derived the partial charges using antechamber and red server. I 
>> next check the density of pure iso propanol and used the closest definition 
>> to the real value. Iso propanol is used as co-solvent with water with a 
>> water:iso propanol ration of 90:10. I will just use my derived parameters 
>> then.
>> 
>> Thanks for your replies.
>> 
>> Max
>> 
>>> On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban  wrote:
>>> 
>>> Normally, this sort of things is done via mechanical combining of the
>>> known groups --  CH3, -CH, OH -- from the force field.
>>> 
>>> If your goal is to increase accuracy for pure 2-propanol per se, then
>>> play with the distribution of electronic density between OH and CH.
>>> 
>>> If 2-propanol is to be used as a solvent for somwthing else, this does
>>> ultimately not pay off.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian  
>>>> wrote:
>>>> I saw the papers you mentioned but one is a not clear how they 
>>>> parameterized, one is missing the supporting material and the last is not 
>>>> showing the parameters they used. I will check with the initial paper of 
>>>> Jorgensen again but if I recall it correctly he mentioned some problems 
>>>> with iso-propanol.
>>>> 
>>>> strange that such a common organic solvent is not easily accessible for 
>>>> OPLS.
>>>> 
>>>> thanks for your help johnny!
>>>> 
>>>> Max
>>>> 
>>>>> On Sep 1, 2015, at 11:41 PM, Johnny Lu  wrote:
>>>>> 
>>>>> that was by google. I haven't parametrized forcefields.
>>>>> did they just put the pieces in
>>>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
>>>>> for 2-propanol?
>>>>> 
>>>>> 
>>>>>> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu  
>>>>>> wrote:
>>>>>> 
>>>>>> Not sure if those are for 2-propanol as a liquid or interaction between
>>>>>> 2-propanol and protein.
>>>>>> from googling "2 propanol opls/aa"
>>>>>> 
>>>>>> 1. Development and Testing of the OPLS All-Atom Force Field on
>>>>>> Conformational Energetics and Properties of Organic Liquids
>>>>>>The parameters are in the supporting info.
>>>>>>Seems not exactly 2-propanol. But it has parameter for organic
>>>>>> liquids.
>>>>>>"OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
>>>>>>http://pubs.acs.org/doi/abs/10.1021/ja9621760
>>>>>> 
>>>>>> 2. A statistical model of hydrogen bond networks in liquid alcohols
>>>>>> 
>>>>>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf
>>>>>> 
>>>>>> 3. Parameterization of OPLS–AA Force Field for the Conformational 
>>>>>> Analysis
>>>>>> of Macrocy

Re: [gmx-users] OPLS/AA parameters for 2-propanol

[Ebert Maximilian]

Hi justin,

thank you for the answer. From your experience to calculate the shear viscosity 
with gmx tcaf for the correction term your mentioned (2.837297kBT/(6πηL)) would 
a trajectory with coordinates and velocities every 1 ps enough?

Thanks

On Sep 2, 2015, at 9:55 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/2/15 9:47 PM, Ebert Maximilian wrote:
Thanks for the answer again. So I saw that for self-diffusion and viscosity I 
can just use gmx tcaf and gmx msd. As an experimental setup, would a squared 
box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good 
system to use tcaf and msd?


Remember to correct for finite size effects in the diffusion constant 
(dx.doi.org/10.1021/jp0477147<http://dx.doi.org/10.1021/jp0477147>)

For the heat of vaporization I saw that I could calculate DHvap =  - 
 + RT

  is just Epot of the same MD I described above but for  I need a 
new calculation. If I understood it correctly I would need a box with the same 
number of molecules as in the previous calculation but separate them with a lot 
of space (50nm was suggested). In addition, turn off PBC, PME, L-J and coulomb 
cut-offs. Get Epot from this calculation and use the formular.


More simply, divide  by the number of molecules and just simulate one 
molecule in the gas phase (infinite cutoffs, no PBC) for .

-Justin

Would these approaches be correct?

Thank you very much.

Max

On Sep 2, 2015, at 5:02 PM, Vitaly V. Chaban 
mailto:vvcha...@gmail.com>> wrote:

It is difficult to get a very wrong density, especially for relatively
rigid compounds. In the meantime, deviations of density within 2% of
the experimental value should be admitted acceptable.

A better criterion is to compare self-diffusion or viscosity to the
experiment. Another famous property for parametrization is heat of
vaporization.






On Wed, Sep 2, 2015 at 3:22 PM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:
Thanks for the reply. I think I found relatively good atom types for iso 
propanol and derived the partial charges using antechamber and red server. I 
next check the density of pure iso propanol and used the closest definition to 
the real value. Iso propanol is used as co-solvent with water with a water:iso 
propanol ration of 90:10. I will just use my derived parameters then.

Thanks for your replies.

Max

On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban 
mailto:vvcha...@gmail.com>> wrote:

Normally, this sort of things is done via mechanical combining of the
known groups --  CH3, -CH, OH -- from the force field.

If your goal is to increase accuracy for pure 2-propanol per se, then
play with the distribution of electronic density between OH and CH.

If 2-propanol is to be used as a solvent for somwthing else, this does
ultimately not pay off.








On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>> wrote:
I saw the papers you mentioned but one is a not clear how they parameterized, 
one is missing the supporting material and the last is not showing the 
parameters they used. I will check with the initial paper of Jorgensen again 
but if I recall it correctly he mentioned some problems with iso-propanol.

strange that such a common organic solvent is not easily accessible for OPLS.

thanks for your help johnny!

Max

On Sep 1, 2015, at 11:41 PM, Johnny Lu 
mailto:johnny.lu...@gmail.com>> wrote:

that was by google. I haven't parametrized forcefields.
did they just put the pieces in
http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
for 2-propanol?


On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu 
mailto:johnny.lu...@gmail.com>> wrote:

Not sure if those are for 2-propanol as a liquid or interaction between
2-propanol and protein.
from googling "2 propanol opls/aa"

1. Development and Testing of the OPLS All-Atom Force Field on
Conformational Energetics and Properties of Organic Liquids
   The parameters are in the supporting info.
   Seems not exactly 2-propanol. But it has parameter for organic
liquids.
   "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
   http://pubs.acs.org/doi/abs/10.1021/ja9621760

2. A statistical model of hydrogen bond networks in liquid alcohols

http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf

3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
of Macrocyclic Polyketides
   https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf

On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian 
wrote:

Dear list,

I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
format. Before deriving my own I thought it would be best to ask first. I
saw some posts that people used 2-propanol in OPLS but couldn’t find any
reference in google scholar.

Thank you very much,

Max
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[gmx-users] Creating a box of water with density 1000 g/l

[Ebert Maximilian]

Hi there,

I am wondering if there is a better way to create a box with water of a certain 
size than:

gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512

To get a density of roughly 1000 g/l i would need to add 512 molecules in such 
a box. But the script only adds 502. I could play with the scale parameter but 
sometimes I have problems during minimization with messages like:

Water molecule starting at atom 1465 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Thank you very much,

Max

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Re: [gmx-users] Creating a box of water with density 1000 g/l

[Ebert Maximilian]

The reason is that I try to reproduce the experiment from the paper System-Size 
Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics
Simulations with Periodic Boundary Conditions.

before calculating the self diffusion coefficient for my organic solvent i 
wanted to see if my system setup is correct. the authors used 33 water 
molecules per nm^3. Therefore, I try to create a box in GROMACS with L=2.494 
and fit 512 molecules of TIP3P water in. The reason the authors used these 33 
molecules is to get about 1bar during the NVT without barostat.

Max

> On Sep 10, 2015, at 4:56 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 9/10/15 4:44 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am wondering if there is a better way to create a box with water of a 
>> certain size than:
>> 
>> gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512
>> 
>> To get a density of roughly 1000 g/l i would need to add 512 molecules in 
>> such a box. But the script only adds 502. I could play with the scale 
>> parameter but sometimes I have problems during minimization with messages 
>> like:
>> 
>> Water molecule starting at atom 1465 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> 
> 
> The density will anyway be dictated by the water model itself; none of the 
> common ones achieve exactly 1000 g/L.  In principle, you could expand the box 
> very slightly, then re-size the box and simulate with NVT (thus constant 
> density), but at that point you're really manipulating the outcome, and I 
> don't know why you would need to go to such lengths.
> 
> -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] Creating a box of water with density 1000 g/l

[Ebert Maximilian]

Thanks for the reply. I think I can simulate it now. The only thing I don’t 
understand and this is in reference to my other post: OPLS/AA parameters for 
2-propanol
How can the self-diffusion coefficient be a good measure for testing my 
parameters if for TIP3P water the self-diffusion coefficient ist 6 x 10^-9 m2 
s-1 but the experimental value is around 2.3 x 10^-9 m2 s-1. So if even for a 
highly used water model the coefficient doesn’t fit how can I make any 
assumption about the quality of my parameters for 2-propanol?

Thanks



On Sep 10, 2015, at 5:15 PM, Phwey Gil mailto:ps...@case.edu>> 
wrote:

I think I would do it this way.

Use L that is slightly larger than 2.494 so that you can fit all of the
512 water molecules you want. Then run a very short simulation at 10 bar.
The size of the box now should be less than 2.494.

Now change the box size to 2.494 and then run the final equilibration step
with NVT ensemble.

Run the simulation and then see if you get 1 bar!

On Thursday, September 10, 2015, Ebert Maximilian 
mailto:m.eb...@umontreal.ca>>
wrote:

The reason is that I try to reproduce the experiment from the paper
System-Size Dependence of Diffusion Coefficients and Viscosities from
Molecular Dynamics
Simulations with Periodic Boundary Conditions.

before calculating the self diffusion coefficient for my organic solvent i
wanted to see if my system setup is correct. the authors used 33 water
molecules per nm^3. Therefore, I try to create a box in GROMACS with
L=2.494 and fit 512 molecules of TIP3P water in. The reason the authors
used these 33 molecules is to get about 1bar during the NVT without
barostat.

Max

On Sep 10, 2015, at 4:56 PM, Justin Lemkul 
mailto:jalem...@vt.edu>
> wrote:



On 9/10/15 4:44 PM, Ebert Maximilian wrote:
Hi there,

I am wondering if there is a better way to create a box with water of a
certain size than:

gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512

To get a density of roughly 1000 g/l i would need to add 512 molecules
in such a box. But the script only adds 502. I could play with the scale
parameter but sometimes I have problems during minimization with messages
like:

Water molecule starting at atom 1465 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.


The density will anyway be dictated by the water model itself; none of
the common ones achieve exactly 1000 g/L.  In principle, you could expand
the box very slightly, then re-size the box and simulate with NVT (thus
constant density), but at that point you're really manipulating the
outcome, and I don't know why you would need to go to such lengths.

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

==
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[gmx-users] Load GROMACS trajectory with atom types and water in VMD

[Ebert Maximilian]

Dear list, 

I am not sure if this is a question for the VMD or GROMACS mailing list. 
However, I try to load a trr/xtc trajectory into VMD and want to keep the atom 
types. Since top and tpr files are not an input for VMD the atom type and name 
is the same as the structure file is PDB or GRO. I also tried top2psf but I 
guess since I have water and need the water in the trajectory I can’t use the 
script. Any idea how I could load the atom types?

Thank you very much. 

Max

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Re: [gmx-users] Load GROMACS trajectory with atom types and water in VMD

[Ebert Maximilian]

Hi,

for the implicit ligand sampling module in VMD you need a loaded trajectory 
with the correct atom types. i guess I have to load them manually from another 
file into VMD.

Max

> On Sep 24, 2015, at 4:43 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> You can get what is in the structure file, and that is all. Since the atom
> name is not the name of the force-field atom type, I don't think you can do
> what you want. It is likely that whatever you were planning to do with atom
> types you can do with the VMD selection syntax.
> 
> Mark
> 
> On Thu, Sep 24, 2015 at 10:28 PM Ebert Maximilian 
> wrote:
> 
>> Dear list,
>> 
>> I am not sure if this is a question for the VMD or GROMACS mailing list.
>> However, I try to load a trr/xtc trajectory into VMD and want to keep the
>> atom types. Since top and tpr files are not an input for VMD the atom type
>> and name is the same as the structure file is PDB or GRO. I also tried
>> top2psf but I guess since I have water and need the water in the trajectory
>> I can’t use the script. Any idea how I could load the atom types?
>> 
>> Thank you very much.
>> 
>> Max
>> 
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[gmx-users] Free oxygen in water AMBER FF definition to use in GROMACS

[Ebert Maximilian]

Hi there,

I wanted to know if anyone has AMBER FF definition of oxygen, which I could use 
to simulate oxygen in water. 

Thank you very much,

Max

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[gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme 
parameters in the mol2 and frcmod file format. I know that I can generate .itp 
files containing the parameters, which I can later add to my .top file. 
However, it would be much easier to use pdb2gmx directly without stripping the 
heme and the cysteine binding the heme and later manually add it again. I added 
the cysteine to the standard amber force field. However, before adding the heme 
manually I wanted to know if there is a way to load an itp file while executing 
pdb2gmx?

How would you add the information from the cysteine in mol2 format and the heme 
in mol2/frcmod format to amber in gromacs?

Thank you very much,

Max
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Re: [gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF 
FF to work in GROMACS? I would need all the bonded and non bonded definitions 
of GAFF for the heme in der AMBER FF port in GROMACS right?

Max

> On Sep 25, 2015, at 1:36 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am trying to simulate a heme containing protein. I found AMBER heme
>> parameters in the mol2 and frcmod file format. I know that I can generate
>> .itp files containing the parameters, which I can later add to my .top file.
>> However, it would be much easier to use pdb2gmx directly without stripping
>> the heme and the cysteine binding the heme and later manually add it again. I
>> added the cysteine to the standard amber force field. However, before adding
>> the heme manually I wanted to know if there is a way to load an itp file
>> while executing pdb2gmx?
>> 
> 
> pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
> ffbonded.itp or ffnonbonded.itp as needed.
> 
>> How would you add the information from the cysteine in mol2 format and the
>> heme in mol2/frcmod format to amber in gromacs?
>> 
> 
> Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys 
> is already supported via specbond.dat.
> 
> -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] GROMACS with AMBER heme parameters

[Ebert Maximilian]

I read that and this is the way I added the cysteine to AMBER which connects to 
the heme. Now I am adding the heme but the FF definition for bonds, angles, etc 
are all in lower case for the GAFF FF. From you answer I guess I need to add 
these lower case atom types and the bonds, angles, etc definition from the GAFF 
FF to the AMBER FF manually.

Not much fun but I will share the work here in the end. Maybe this will help 
people who want to simulate heme containing proteins in GROMACS and 
AMBER99SB-ILDN.

Have a good weekend,
Max


On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/25/15 4:22 PM, Ebert Maximilian wrote:
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF 
FF to work in GROMACS? I would need all the bonded and non bonded definitions 
of GAFF for the heme in der AMBER FF port in GROMACS right?


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

-Justin

Max

On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/25/15 1:32 PM, Ebert Maximilian wrote:
Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without stripping
the heme and the cysteine binding the heme and later manually add it again. I
added the cysteine to the standard amber force field. However, before adding
the heme manually I wanted to know if there is a way to load an itp file
while executing pdb2gmx?


pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
ffbonded.itp or ffnonbonded.itp as needed.

How would you add the information from the cysteine in mol2 format and the
heme in mol2/frcmod format to amber in gromacs?


Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys is 
already supported via specbond.dat.

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

==
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==

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

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

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

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Re: [gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Yeah that is what I thought but that’s life. 

One more question.In the [ atomtypes ] section I need the sigma and epsilon 
value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is in 
nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in 
angstroem and defined as r0 which is sigma *( the 6th root of 2). 

So I picked an atomtype which is defined in the same way in AMBER and GAFF to 
see if I am doing the conversion right. A standard carbon CA is similar in both 
since the definition is taken from OPLS:

GAFF ca  r0: 1.9080  epsilon: 0.0860

If I look in the AMBER FF in GROMACS this changes to 

AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01

If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as 
expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, 
which is half. Why is the sigma value in GROMACS two times the sigma value in 
GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just wanted 
to be sure.

Thanks

> On Sep 25, 2015, at 4:43 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 9/25/15 4:40 PM, Ebert Maximilian wrote:
>> I read that and this is the way I added the cysteine to AMBER which connects 
>> to the heme. Now I am adding the heme but the FF definition for bonds, 
>> angles, etc are all in lower case for the GAFF FF. From you answer I guess I 
>> need to add these lower case atom types and the bonds, angles, etc 
>> definition from the GAFF FF to the AMBER FF manually.
>> 
> 
> Indeed, which is what steps 3 and 4 tell you.  Adding a residue is simple, 
> but if that residue involves modifications to the force field, then there is 
> more work to be done.
> 
> -Justin
> 
>> Not much fun but I will share the work here in the end. Maybe this will help 
>> people who want to simulate heme containing proteins in GROMACS and 
>> AMBER99SB-ILDN.
>> 
>> Have a good weekend,
>> Max
>> 
>> 
>> On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
>> mailto:jalem...@vt.edu>> wrote:
>> 
>> 
>> 
>> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
>> Since the heme definition in AMBER uses GAFF atom types how do I get the 
>> GAFF FF to work in GROMACS? I would need all the bonded and non bonded 
>> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>> 
>> 
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>> 
>> -Justin
>> 
>> Max
>> 
>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
>> mailto:jalem...@vt.edu>> wrote:
>> 
>> 
>> 
>> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am trying to simulate a heme containing protein. I found AMBER heme
>> parameters in the mol2 and frcmod file format. I know that I can generate
>> .itp files containing the parameters, which I can later add to my .top file.
>> However, it would be much easier to use pdb2gmx directly without stripping
>> the heme and the cysteine binding the heme and later manually add it again. I
>> added the cysteine to the standard amber force field. However, before adding
>> the heme manually I wanted to know if there is a way to load an itp file
>> while executing pdb2gmx?
>> 
>> 
>> pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
>> ffbonded.itp or ffnonbonded.itp as needed.
>> 
>> How would you add the information from the cysteine in mol2 format and the
>> heme in mol2/frcmod format to amber in gromacs?
>> 
>> 
>> Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys 
>> is already supported via specbond.dat.
>> 
>> -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<mailto:jalem...@outerbanks.umaryland.edu> 
>> | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> ==
>> --
>> Gromacs Users mailing list
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Re: [gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

I will answer my own question: I found in another post that indeed in GROMACS 
its Rmin. 

Thanks

> On Sep 25, 2015, at 5:25 PM, Ebert Maximilian  wrote:
> 
> Yeah that is what I thought but that’s life. 
> 
> One more question.In the [ atomtypes ] section I need the sigma and epsilon 
> value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is 
> in nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in 
> angstroem and defined as r0 which is sigma *( the 6th root of 2). 
> 
> So I picked an atomtype which is defined in the same way in AMBER and GAFF to 
> see if I am doing the conversion right. A standard carbon CA is similar in 
> both since the definition is taken from OPLS:
> 
> GAFF ca  r0: 1.9080  epsilon: 0.0860
> 
> If I look in the AMBER FF in GROMACS this changes to 
> 
> AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01
> 
> If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as 
> expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, 
> which is half. Why is the sigma value in GROMACS two times the sigma value in 
> GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just 
> wanted to be sure.
> 
> Thanks
> 
>> On Sep 25, 2015, at 4:43 PM, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 9/25/15 4:40 PM, Ebert Maximilian wrote:
>>> I read that and this is the way I added the cysteine to AMBER which 
>>> connects to the heme. Now I am adding the heme but the FF definition for 
>>> bonds, angles, etc are all in lower case for the GAFF FF. From you answer I 
>>> guess I need to add these lower case atom types and the bonds, angles, etc 
>>> definition from the GAFF FF to the AMBER FF manually.
>>> 
>> 
>> Indeed, which is what steps 3 and 4 tell you.  Adding a residue is simple, 
>> but if that residue involves modifications to the force field, then there is 
>> more work to be done.
>> 
>> -Justin
>> 
>>> Not much fun but I will share the work here in the end. Maybe this will 
>>> help people who want to simulate heme containing proteins in GROMACS and 
>>> AMBER99SB-ILDN.
>>> 
>>> Have a good weekend,
>>> Max
>>> 
>>> 
>>> On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
>>> mailto:jalem...@vt.edu>> wrote:
>>> 
>>> 
>>> 
>>> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
>>> Since the heme definition in AMBER uses GAFF atom types how do I get the 
>>> GAFF FF to work in GROMACS? I would need all the bonded and non bonded 
>>> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>>> 
>>> 
>>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>> 
>>> -Justin
>>> 
>>> Max
>>> 
>>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
>>> mailto:jalem...@vt.edu>> wrote:
>>> 
>>> 
>>> 
>>> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>>> Hi there,
>>> 
>>> I am trying to simulate a heme containing protein. I found AMBER heme
>>> parameters in the mol2 and frcmod file format. I know that I can generate
>>> .itp files containing the parameters, which I can later add to my .top file.
>>> However, it would be much easier to use pdb2gmx directly without stripping
>>> the heme and the cysteine binding the heme and later manually add it again. 
>>> I
>>> added the cysteine to the standard amber force field. However, before adding
>>> the heme manually I wanted to know if there is a way to load an itp file
>>> while executing pdb2gmx?
>>> 
>>> 
>>> pdb2gmx does not need .itp information.  grompp does.  Add the parameters 
>>> to ffbonded.itp or ffnonbonded.itp as needed.
>>> 
>>> How would you add the information from the cysteine in mol2 format and the
>>> heme in mol2/frcmod format to amber in gromacs?
>>> 
>>> 
>>> Charges and connectivity go in the .rtp entry.  Heme ligation by His and 
>>> Cys is already supported via specbond.dat.
>>> 
>>> -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 

Re: [gmx-users] Topology for ligands

[Ebert Maximilian]

maybe this could be a good staring point:

http://www.esi.umontreal.ca/~pelletjo/gromacs/derive01.html


On Sep 26, 2015, at 5:14 PM, Juliano Braz Carregal 
mailto:julianocarre...@hotmail.com>> wrote:


Can someone tell me a good program/sever besides prodg ,to generate topology 
for organic and inorganic ligands.thanks

Em 26/09/2015 2:48 PM, 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se
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Today's Topics:

   1. bonded forces in output (Stanislav ?imko)
   2. Re: bonded forces in output (Justin Lemkul)
   3. Installation problem
  (Parham Jabbarzadeh (Department of Biomedical Science))
   4. Restart simulation after crash (Juliano Braz Carregal)
   5. Re: Restart simulation after crash (Justin Lemkul)


--

Message: 1
Date: Sat, 26 Sep 2015 11:31:24 +0200
From: Stanislav ?imko 
mailto:stanislav.si...@gmail.com>>
To: 
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] bonded forces in output
Message-ID: 
<1443259884.25179.9.ca...@gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear gromacs users,
I'm writing my code to calculate pressure from trajectory files - from
problthat em atomic positions and forces - according to virial theorem.
Currently, I'm able to calculate the same pressure when I've got only
non-bonded forces of a small system (10 atoms with charges and LJ
parameters) centered in a big (100nm cubic) box. Hopefully, my code
should work also for smaller box where atoms can see periodic images.
The problem that I'm facing right now is that I do not know how to
obtain bonded forces from the trajectory files. E.g., for single spc
water molecule gromacs gives zero forces on all atoms, even though I
assigned them different velocities.
to obtain forces I run:
gmx traj -f *.trr -s *.tpr -of forces -fp
 Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),
which means that there are some forces
gmx energy -f *.edr -s *.tpr ...
So I would like to ask, if there is some way how to get bonded forces
out of the trajectory... (or rerun with some runtime parameters to
force gromacs to print bonded forces)
Sincerely,
stanislav.


--

Message: 2
Date: Sat, 26 Sep 2015 12:02:48 -0400
From: Justin Lemkul mailto:jalem...@vt.edu>>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] bonded forces in output
Message-ID: <5606c1a8.4090...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 9/26/15 5:31 AM, Stanislav ?imko wrote:
> Dear gromacs users,
> I'm writing my code to calculate pressure from trajectory files - from
> problthat em atomic positions and forces - according to virial theorem.
> Currently, I'm able to calculate the same pressure when I've got only
> non-bonded forces of a small system (10 atoms with charges and LJ
> parameters) centered in a big (100nm cubic) box. Hopefully, my code
> should work also for smaller box where atoms can see periodic images.
> The problem that I'm facing right now is that I do not know how to
> obtain bonded forces from the trajectory files. E.g., for single spc
> water molecule gromacs gives zero forces on all atoms, even though I
> assigned them different velocities.
>to obtain forces I run:
>gmx traj -f *.trr -s *.tpr -of forces -fp
>   Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),
> which means that there are some forces
>gmx energy -f *.edr -s *.tpr ...
> So I would like to ask, if there is some way how to get bonded forces
> out of the trajectory... (or rerun with some runtime parameters to
> force gromacs to print bonded forces)

By default, water is treated as rigid via SETTLE, so there are no bonded forces.
  You can turn this off with "define = -DFLEXIBLE" in the .mdp file for the
purpose of do a re-calculation of energies and forces.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirsc

[gmx-users] Insert molecules in system with minimum distance between them

[Ebert Maximilian]

Dear list,

I am trying to add n-number of molecules in my prepare protein+water+ions box 
but keep a minimum distance of 1 nm in all directions between the newly 
inserted molecules. On top of that I want to replace solvent molecules with the 
newly added molecules. So basically I am looking for gmx genion with the -rmin 
flag for non ions.
Which tool could I use?

Thanks,
Max
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[gmx-users] GMXLIB does not induce residuetype.dat

[Ebert Maximilian]

Dear list,

I have my own force field working folder so I cloned the entire top folder to 
no mess with the original files. I added residues to the residue type file to 
add my residues to the protein group. My FF is included due to the GMXLIB 
environmental variable but my modified residuestype.dat not. Any idea why?

Thanks
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Re: [gmx-users] GMXLIB does not induce residuetype.dat

[Ebert Maximilian]

thanks for the answer. in the console i wrote:

GMXLIB="~/GROMACS/gromacs_ff/“
export GMXLIB

the shell is GNU bash, version 4.1.2(1)-release

Max



> On Oct 2, 2015, at 9:22 AM, João M. Damas  wrote:
> 
> How are you defining the GMXLIB variable in your script? Please give us
> some more information (inputs and outputs) for us to be able to help you.
> 
> João
> 
> On Thu, Oct 1, 2015 at 9:21 PM, Ebert Maximilian 
> wrote:
> 
>> Dear list,
>> 
>> I have my own force field working folder so I cloned the entire top folder
>> to no mess with the original files. I added residues to the residue type
>> file to add my residues to the protein group. My FF is included due to the
>> GMXLIB environmental variable but my modified residuestype.dat not. Any
>> idea why?
>> 
>> Thanks
>> --
>> 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.
>> 
> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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Re: [gmx-users] Free oxygen in water AMBER FF definition to use in GROMACS

[Ebert Maximilian]

I found a definition for oxygen in the paper: Effective Simulations of Gas 
Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 
Pathways and Escape Routes in T-state Deoxyhemoglobin 

they use CHARMM as FF and I will use AMBER99SB-ILDN so not ideal because it was 
not calculate with the same FF in mind but for such a simple molecule it should 
be fine.

have a good weekend,

max


> On Sep 24, 2015, at 5:59 PM, Ebert Maximilian  wrote:
> 
> Hi there,
> 
> I wanted to know if anyone has AMBER FF definition of oxygen, which I could 
> use to simulate oxygen in water. 
> 
> Thank you very much,
> 
> Max
> 
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[gmx-users] Possibility to keep molecules during MD at a certain distance

[Ebert Maximilian]

Hi list,

I am trying to enforce a minimum pair distance of certain molecules in my MD 
using a network of repulsive half-harmonic distance-restraining potentials with 
a specific force constant. How would I do that? Is it the [ bonds ] type 6 
option? If so do I have to write a bond for each molecule with each molecule?

Thanks for the help
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[gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

Hi there,

I want to calculate ht RMSF of the carbon alpha. First which atoms are used if 
I calculate the RMSF per residue with -res and how can I calculate the RMSF of 
carbon alpha or NH vector etc? Can’t seem to find an input except for the group 
of the alignment for the -fit 

Thank you,

Max
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Re: [gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

I think I can answer my own question again. The group you use for root mean 
square calculation is also the RMSF group. If the group has more than one atom 
per residue and I use -res I get the average RMSF of all atoms per residue. 

Hope this is correct.

Max

> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian  wrote:
> 
> Hi there,
> 
> I want to calculate ht RMSF of the carbon alpha. First which atoms are used 
> if I calculate the RMSF per residue with -res and how can I calculate the 
> RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except for 
> the group of the alignment for the -fit 
> 
> Thank you,
> 
> Max
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Re: [gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

Oh infact no thats not the case it is still the RMSF of all atoms in the 
residue. So back to my initial question. How can I calculate the RMSF on the Ca 
of each residue?

Sorry if this caused any confusion.

Max

> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian  wrote:
> 
> I think I can answer my own question again. The group you use for root mean 
> square calculation is also the RMSF group. If the group has more than one 
> atom per residue and I use -res I get the average RMSF of all atoms per 
> residue. 
> 
> Hope this is correct.
> 
> Max
> 
>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian  wrote:
>> 
>> Hi there,
>> 
>> I want to calculate ht RMSF of the carbon alpha. First which atoms are used 
>> if I calculate the RMSF per residue with -res and how can I calculate the 
>> RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except 
>> for the group of the alignment for the -fit 
>> 
>> Thank you,
>> 
>> Max
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Re: [gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

Thanks for the clarification Tsjerk. So my previous assumption was right. 
Basically if I want to align on the backbone but want the RMSF of Calpha I need 
to align first, save the trajectory and do RMSF with -nofit right?

Max

> On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar  wrote:
> 
> Hi Ebert,
> 
> Use C-alpha as the group. Yes, it will be used for fitting and calculation
> of the RMSF.
> 
> Cheers,
> 
> Tsjerk
> On Oct 5, 2015 22:44, "Ebert Maximilian"  wrote:
> 
>> Oh infact no thats not the case it is still the RMSF of all atoms in the
>> residue. So back to my initial question. How can I calculate the RMSF on
>> the Ca of each residue?
>> 
>> Sorry if this caused any confusion.
>> 
>> Max
>> 
>>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian 
>> wrote:
>>> 
>>> I think I can answer my own question again. The group you use for root
>> mean square calculation is also the RMSF group. If the group has more than
>> one atom per residue and I use -res I get the average RMSF of all atoms per
>> residue.
>>> 
>>> Hope this is correct.
>>> 
>>> Max
>>> 
>>>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian 
>> wrote:
>>>> 
>>>> Hi there,
>>>> 
>>>> I want to calculate ht RMSF of the carbon alpha. First which atoms are
>> used if I calculate the RMSF per residue with -res and how can I calculate
>> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input
>> except for the group of the alignment for the -fit
>>>> 
>>>> Thank you,
>>>> 
>>>> Max
>>>> --
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>> posting!
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Re: [gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

Like gmx rms the gmx rmsf tool should be extended to align and calculate on 
different index groups. That would be helpful. Also maybe we could add some 
information about the -res flag and the behaviour for aligning and calculating 
the the gmx rmsf help text. How could I suggest that officially?

Max

> On Oct 6, 2015, at 2:36 AM, Tsjerk Wassenaar  wrote:
> 
> Right :)
> 
> Cheers,
> 
> Tsjerk
> 
> On Mon, Oct 5, 2015 at 11:07 PM, Ebert Maximilian 
> wrote:
> 
>> Thanks for the clarification Tsjerk. So my previous assumption was right.
>> Basically if I want to align on the backbone but want the RMSF of Calpha I
>> need to align first, save the trajectory and do RMSF with -nofit right?
>> 
>> Max
>> 
>>> On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar  wrote:
>>> 
>>> Hi Ebert,
>>> 
>>> Use C-alpha as the group. Yes, it will be used for fitting and
>> calculation
>>> of the RMSF.
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> On Oct 5, 2015 22:44, "Ebert Maximilian"  wrote:
>>> 
>>>> Oh infact no thats not the case it is still the RMSF of all atoms in the
>>>> residue. So back to my initial question. How can I calculate the RMSF on
>>>> the Ca of each residue?
>>>> 
>>>> Sorry if this caused any confusion.
>>>> 
>>>> Max
>>>> 
>>>>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian 
>>>> wrote:
>>>>> 
>>>>> I think I can answer my own question again. The group you use for root
>>>> mean square calculation is also the RMSF group. If the group has more
>> than
>>>> one atom per residue and I use -res I get the average RMSF of all atoms
>> per
>>>> residue.
>>>>> 
>>>>> Hope this is correct.
>>>>> 
>>>>> Max
>>>>> 
>>>>>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian 
>>>> wrote:
>>>>>> 
>>>>>> Hi there,
>>>>>> 
>>>>>> I want to calculate ht RMSF of the carbon alpha. First which atoms are
>>>> used if I calculate the RMSF per residue with -res and how can I
>> calculate
>>>> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input
>>>> except for the group of the alignment for the -fit
>>>>>> 
>>>>>> Thank you,
>>>>>> 
>>>>>> Max
>>>>>> --
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Re: [gmx-users] Gromacs

[Ebert Maximilian]

Maybe you should start telling is which force field you are trying to use. 
GROMACS provides 15 different.

Max

> On Oct 6, 2015, at 1:51 AM, saranya  wrote:
> 
> GROMACS users,
> 
> I was trying to perform a MD simulation of a system with a protein with Ag+
> metal ion but realized that GROMACS does not  have parameters for the Ag+
> ion. I tried to include the parameters in the ion.itp file but did not
> succeed yet. Does anyone knows the right procedure to introduce this ions
> into the file ions.itp? do we have to change anything more in order to
> GROMACS recognize the new ion?
> 
> With Regards
> 
> *Saranya Vasudevan,*
> 
> *Research Scholar,*
> 
> *Molecular Quantum Mechanics Laboratory,*
> 
> *Department of Physics,*
> 
> *Bharathiar University,*
> 
> *Coimbatore-46*
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Re: [gmx-users] GMXLIB does not induce residuetype.dat

[Ebert Maximilian]

Hi,
sorry for responding that late. The problem in the end was that first in 
specbonds the search length was 0.1nm off so it appeared for this structure as 
if the file wasn’t used but it was. and second i had the merge the PDB chain 
since there was a TER between the hetero atom and the protein residues.

so now all is good. putting in ~/.bash_profile 

GMXLIB=

works fine. Thanks for your help,

Max

> On Oct 3, 2015, at 1:03 PM, João M. Damas  wrote:
> 
> The definition seems fine. In the pdb2gmx standard output, you should check
> that directory is the one being opened.
> 
> If it is, please do a "ls ${GMXLIB}" and check the output, if the file is
> there (and not inside the ff directory). Even though I am guessing this is
> just a typo problem, and you are using "residuestype.dat" while the file is
> "residuetypes.dat".
> 
> João
> 
> On Sat, Oct 3, 2015 at 4:55 AM, Barnett, James W 
> wrote:
> 
>> On Thu, 2015-10-01 at 20:21 +, Ebert Maximilian wrote:
>>> Dear list,
>>> 
>>> I have my own force field working folder so I cloned the entire top
>> folder to
>>> no mess with the original files. I added residues to the residue type
>> file to
>>> add my residues to the protein group. My FF is included due to the GMXLIB
>>> environmental variable but my modified residuestype.dat not. Any idea
>> why?
>> 
>> Can you give an example of how it is not included? Is there a specific
>> GROMACS
>> command that is not finding it, or is it something else?
>> 
>> --
>> James “Wes” Barnett, Ph.D. Candidate
>> Louisiana Board of Regents Fellow
>> 
>> Chemical and Biomolecular Engineering
>> Tulane University
>> 341-B Lindy Boggs Center for Energy and Biotechnology
>> 6823 St. Charles Ave
>> New Orleans, Louisiana 70118-5674
>> jbarn...@tulane.edu
>> --
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>> 
> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Ebert Maximilian]

Dear list, 

I already asked the question in the AMBER list but couldn’t get an answer. So I 
try my luck here even though it is a bit off topic in the GROMACS list. I was 
wondering why the different atom types of H, C and O have different 
LJ-parameter but for all the different types of N we see the identical 
parameters in OPLS, AMBER and CHARMM?

Thank you very much,

Max
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Re: [gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Ebert Maximilian]

Thanks for the answer. I was checking the CHARMM22 All-Hydrogen Parameter File 
for Proteins par_all22_prot.inp and the section non-bonded:

nitrogens
N  0.00  -0.20 1.85   0.00  -0.000100 1.85 ! 
ALLOW   PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC20.00  -0.20 1.85 ! ALLOW   POL
! JG 8/27/89; note: NH1 in ARG was changed to NC2.
NH10.00  -0.20 1.85   0.00  -0.20 1.55 ! 
ALLOW   PEP POL ARO
! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
NH20.00  -0.20 1.85 ! ALLOW   POL
! adm jr.
NH30.00  -0.20 1.85 ! ALLOW   POL
! adm jr.
NP 0.00  -0.20 1.85 ! ALLOW  PRO
! N-terminal proline; from 6-31g* +ProNH2  RLD 9/28/90
NPH0.00  -0.20 1.85 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR10.00  -0.20 1.85 ! ALLOW ARO
! His, adm jr., 9/4/89
NR20.00  -0.20 1.85 ! ALLOW ARO
! His, adm jr., 9/4/89
NR30.00  -0.20 1.85 ! ALLOW ARO
! His, adm jr., 9/4/89
NY 0.00  -0.20 1.85 ! ALLOW   ARO
! trp, JWK

All nitrogen have the same LJ parameter. I haven’t checked CGenFF but I will 
definitely look into that. Thanks for you comment.

Max

> On Oct 22, 2015, at 12:40 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 10/22/15 11:04 AM, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I already asked the question in the AMBER list but couldn’t get an answer. 
>> So I try my luck here even though it is a bit off topic in the GROMACS list. 
>> I was wondering why the different atom types of H, C and O have different 
>> LJ-parameter but for all the different types of N we see the identical 
>> parameters in OPLS, AMBER and CHARMM?
>> 
> 
> Sometimes that's just the way force fields work out.  Electrostatics are 
> tuned first, and then condensed phase interactions are targeted for LJ 
> refinement. Given the nature of most N interactions (either lone pair or via 
> polar/hydrogen bonding interactions with an H), the electrostatics generally 
> dominate, so a generic LJ parameter that is common to different moieties is 
> sufficient.
> 
> In CGenFF, there are several N types with different LJ, though the 
> biomolecular parts of the CHARMM force field share the same parameters.
> 
> -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] Verify if position restrain was applied

[Ebert Maximilian]

Dear list,

I wanted to know if there is a way to verify if the position restrain was 
applied correctly to the atoms in question. Couldn’t find anything in the log 
file.

Thank you,

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Re: [gmx-users] Verify if position restrain was applied

[Ebert Maximilian]

I saw that you can use gmx energy to select Position-Rest. and Constr.-rmsd but 
I was looking for the atom id on which the position restrains acted. Looking at 
my trajectory I am not sure if I did the correct configuration since my energy 
from gmx energy -> Position-Rest shows a maximum of 20kJ/mol but my molecule 
moved around its position with a restrain of 1000 1000 1000.

Max

> On Oct 26, 2015, at 4:02 PM, David van der Spoel  wrote:
> 
> On 26/10/15 20:58, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I wanted to know if there is a way to verify if the position restrain was 
>> applied correctly to the atoms in question. Couldn’t find anything in the 
>> log file.
>> 
> How about position restraint energy?
> 
>> Thank you,
>> 
>> > 
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Verify if position restrain was applied

[Ebert Maximilian]

Thank you for your clarification that makes sense now in my simulation. Never 
the less is there an output per atom somewhere?

Thank you very much

> On Oct 26, 2015, at 4:37 PM, David van der Spoel  wrote:
> 
> On 26/10/15 21:06, Ebert Maximilian wrote:
>> I saw that you can use gmx energy to select Position-Rest. and Constr.-rmsd 
>> but I was looking for the atom id on which the position restrains acted. 
>> Looking at my trajectory I am not sure if I did the correct configuration 
>> since my energy from gmx energy -> Position-Rest shows a maximum of 20kJ/mol 
>> but my molecule moved around its position with a restrain of 1000 1000 1000.
>> 
>> Max
>> 
>>> On Oct 26, 2015, at 4:02 PM, David van der Spoel  
>>> wrote:
>>> 
>>> On 26/10/15 20:58, Ebert Maximilian wrote:
>>>> Dear list,
>>>> 
>>>> I wanted to know if there is a way to verify if the position restrain was 
>>>> applied correctly to the atoms in question. Couldn’t find anything in the 
>>>> log file.
>>>> 
> restraint mean 1000 kJ/mol/nm^2, so 20 kJ/mol means 0.02 nm^2, or 0.14 nm for 
> 1 atom.
>>> How about position restraint energy?
>>> 
>>>> Thank you,
>>>> 
>>>> >>> 
>>> 
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> --
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>> 
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Verify if position restrain was applied

[Ebert Maximilian]

Thanks I didn’t know the dump command.

Good evening

On Oct 26, 2015, at 4:50 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 10/26/15 4:44 PM, Ebert Maximilian wrote:
Thank you for your clarification that makes sense now in my simulation. Never 
the less is there an output per atom somewhere?


Everything is in the .tpr file.  Use gmx dump and redirect to a file and look 
through.

-Justin

Thank you very much

On Oct 26, 2015, at 4:37 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:

On 26/10/15 21:06, Ebert Maximilian wrote:
I saw that you can use gmx energy to select Position-Rest. and Constr.-rmsd but 
I was looking for the atom id on which the position restrains acted. Looking at 
my trajectory I am not sure if I did the correct configuration since my energy 
from gmx energy -> Position-Rest shows a maximum of 20kJ/mol but my molecule 
moved around its position with a restrain of 1000 1000 1000.

Max

On Oct 26, 2015, at 4:02 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:

On 26/10/15 20:58, Ebert Maximilian wrote:
Dear list,

I wanted to know if there is a way to verify if the position restrain was 
applied correctly to the atoms in question. Couldn’t find anything in the log 
file.

restraint mean 1000 kJ/mol/nm^2, so 20 kJ/mol means 0.02 nm^2, or 0.14 nm for 1 
atom.
How about position restraint energy?

Thank you,

mailto:sp...@xray.bmc.uu.se>http://folding.bmc.uu.se
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--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>http://folding.bmc.uu.se
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--
==

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

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

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

==
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[gmx-users] gmx chi: chi.log output all rotamers always 0

[Ebert Maximilian]

hi list,

using gmx chi -s file.tpr -f file.xtc -maxchi 1 -all -g -o i try to get the 
different rotamers and transition between them per ns. however, the chi.log 
output file has for every residue only this:

Residue LYS12
Angle [   AI,   AJ,   AK,   AL]  rotamers  0  g(-)  t  g(+)

  Chi1[ 120, 122, 124, 127]0.000.000.000.00


any idea why? the xtc file is aligned and pbc was solved beforehand.

Thank you very much,

Max
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[gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

[Ebert Maximilian]

Dear list,

I tried using g_tune_pme_mpi with the command:

mpirun -np 24 g_tune_pme_mpi -np 24 -s 1ZG4_nvt.tpr -launch

on GROMACS 5.0.1 but I get the following error message:
--
mpirun was unable to launch the specified application as it could not find an 
executable:

Executable: mdrun
Node: 

while attempting to start process rank 0.
--
24 total processes failed to start


Any idea why this is? Shouldn't g_tune_pme_mpi call mdrun_mpi instead?

Thank you very much,

Max
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[gmx-users] AMBER FF naming and caps

[Ebert Maximilian]

Dear list,

I am a little bit confused regarding the preparation needed to use the AMBER FF 
in GROMACS 5.0.1. I have a simple PDB file of a protein and I  use this as 
input to pdb2gmx. I selected the AMBER FF during the creation process:

gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro -water spce

This generates the gro, top and itp file. Now when I open the gro file in VMD I 
get an unusual bond between the last two residues of the protein chain. I 
already figured out why this is. The last amino acid has a charged carboxylate 
with the atom type OC1 and OC2 which are not identified as amino acids by VMD. 
After further reading of the manual I found this paragraph:

The AMBER force fields have unique forms for the terminal residues, and these 
are incompatible with the -ter mechanism. You need to prefix your N- or 
C-terminal residue names with "N" or "C" respectively to use these forms, 
making sure you preserve the format of the coordinate file. Alternatively, use 
named terminating residues (e.g. ACE, NME).

Now I was thinking that I have to change the name of the N and C terminal 
residue. However, looking into my top file GROMACS already knows about AMBER's 
naming convention:

...
; residue 290 TRP rtp CTRP q -1.0
  4049  N290TRP  N   4049-0.3821  14.01   ; qtot 
-6.382
  4050  H290TRP  H   4050 0.2681  1.008   ; qtot 
-6.114
  4051 CT290TRP CA   4051-0.2084  12.01   ; qtot 
-6.322
...

Now my question do I have to do anything or is GROMACS 5 taking care of the 
correct termini in the AMBERE FF?

Thank you very much,

Max
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Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

[Ebert Maximilian]

Hi,

I just tried that and I got the following error message (bench.log). Any idea 
what could be wrong?

Thank you very much,

Max

Initializing Domain Decomposition on 48 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452
  multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452
Minimum cell size due to bonded interactions: 0.464 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm
Estimated maximum distance required for P-LINCS: 0.218 nm

---
Program mdrun_mpi, VERSION 5.0.1
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_setup.c, 
line: 728

Fatal error:
The number of ranks you selected (37) contains a large prime factor 37. In most 
cases this will lead to bad performance. Choose a number with smaller prime 
factors or set the decomposition (option -dd) manually.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten 
Kutzner
Sent: Donnerstag, 25. September 2014 19:29
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

Hi,

don't invoke g_tune_pme with 'mpirun', because it is a serial executable that 
itself invokes parallel MD runs for testing.

use
export MDRUN=mdrun_mpi

g_tune_pme -np 24 -s 1ZG4_nvt.tpr -launch

see also

g_tune_pme -h

You may need to recompile g_tune_pme without MPI enabled (depends on your 
queueing system)

Best,
 Carsten

 
On 25 Sep 2014, at 15:10, Ebert Maximilian  wrote:

> Dear list,
> 
> I tried using g_tune_pme_mpi with the command:
> 
> mpirun -np 24 g_tune_pme_mpi -np 24 -s 1ZG4_nvt.tpr -launch
> 
> on GROMACS 5.0.1 but I get the following error message:
> --
>  mpirun was unable to launch the specified application as it could 
> not find an executable:
> 
> Executable: mdrun
> Node: 
> 
> while attempting to start process rank 0.
> --
> 
> 24 total processes failed to start
> 
> 
> Any idea why this is? Shouldn't g_tune_pme_mpi call mdrun_mpi instead?
> 
> Thank you very much,
> 
> Max
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry Theoretical and Computational 
Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: 
+49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

[Ebert Maximilian]

++ compiler:   /RQusagers/apps/Logiciels/gcc/4.8.1/bin/g++ GNU 4.8.1
C++ compiler flags:  -msse4.1   -std=c++0x -Wextra 
-Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function   
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  
-Wno-array-bounds  -O3 -DNDEBUG
Boost version:  1.55.0 (internal)





  n = 0
   E-zt:
  n = 0
   swapcoords = no
   adress = FALSE
   userint1   = 0
   userint2   = 0
   userint3   = 0
   userint4   = 0
   userreal1  = 0
   userreal2  = 0
   userreal3  = 0
   userreal4  = 0
grpopts:
   nrdf: 10175.6 70836.4
   ref-t:  304.65  304.65
   tau-t: 0.5 0.5
annealing:  Single  Single
annealing-npoints:   4   4
annealing-time [0]:  0.0   200.0   300.0   750.0
annealing-temp [0]: 10.0   100.0   100.0   304.6
annealing-time [1]:  0.0   200.0   300.0   750.0
annealing-temp [1]: 10.0   100.0   100.0   304.6
   acc:0   0   0
   nfreeze:   N   N   N
   energygrp-flags[  0]: 0

Overriding nsteps with value passed on the command line: 1 steps, 0.002 ps


Initializing Domain Decomposition on 48 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452
  multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452
Minimum cell size due to bonded interactions: 0.464 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm
Estimated maximum distance required for P-LINCS: 0.218 nm

---
Program mdrun_mpi, VERSION 5.0.1
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_setup.c, 
line: 728

Fatal error:
The number of ranks you selected (37) contains a large prime factor 37. In most 
cases this will lead to bad performance. Choose a number with smaller prime 
factors or set the decomposition (option -dd) manually.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten 
Kutzner
Sent: Montag, 29. September 2014 15:23
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

Hi,

is this the only output?

Don't you get a perf.out file that lists which settings are optimal?

What exactly was the command line you used?

Carsten


On 29 Sep 2014, at 15:01, Ebert Maximilian  wrote:

> Hi,
> 
> I just tried that and I got the following error message (bench.log). Any idea 
> what could be wrong?
> 
> Thank you very much,
> 
> Max
> 
> Initializing Domain Decomposition on 48 ranks Dynamic load balancing: 
> auto Will sort the charge groups at every domain (re)decomposition 
> Initial maximum inter charge-group distances:
>two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452  
> multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452 
> Minimum cell size due to bonded interactions: 0.464 nm Maximum 
> distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm 
> Estimated maximum distance required for P-LINCS: 0.218 nm
> 
> ---
> Program mdrun_mpi, VERSION 5.0.1
> Source code file: 
> /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_se
> tup.c, line: 728
> 
> Fatal error:
> The number of ranks you selected (37) contains a large prime factor 37. In 
> most cases this will lead to bad performance. Choose a number with smaller 
> prime factors or set the decomposition (option -dd) manually.
> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
> Of Carsten Kutzner
> Sent: Donnerstag, 25. September 2014 19:29
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
> 
> Hi,
> 
> don't invoke g_tune_pme with 'mpirun', because it is a serial executable that 
> itself invokes para

Re: [gmx-users] AMBER FF naming and caps

[Ebert Maximilian]

Thank you very much for your help. This answered my questions.

I wish you a great day,
Max

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Montag, 29. September 2014 14:27
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] AMBER FF naming and caps



On 9/29/14 5:58 AM, Ebert Maximilian wrote:
> Dear list,
>
> I am a little bit confused regarding the preparation needed to use the AMBER 
> FF in GROMACS 5.0.1. I have a simple PDB file of a protein and I  use this as 
> input to pdb2gmx. I selected the AMBER FF during the creation process:
>
> gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro -water spce
>
> This generates the gro, top and itp file. Now when I open the gro file in VMD 
> I get an unusual bond between the last two residues of the protein chain. I 
> already figured out why this is. The last amino acid has a charged 
> carboxylate with the atom type OC1 and OC2 which are not identified as amino 
> acids by VMD. After further reading of the manual I found this paragraph:
>
> The AMBER force fields have unique forms for the terminal residues, and these 
> are incompatible with the -ter mechanism. You need to prefix your N- or 
> C-terminal residue names with "N" or "C" respectively to use these forms, 
> making sure you preserve the format of the coordinate file. Alternatively, 
> use named terminating residues (e.g. ACE, NME).
>
> Now I was thinking that I have to change the name of the N and C terminal 
> residue. However, looking into my top file GROMACS already knows about 
> AMBER's naming convention:
>
> ...
> ; residue 290 TRP rtp CTRP q -1.0
>4049  N290TRP  N   4049-0.3821  14.01   ; qtot 
> -6.382
>4050  H290TRP  H   4050 0.2681  1.008   ; qtot 
> -6.114
>4051 CT290TRP CA   4051-0.2084  12.01   ; qtot 
> -6.322
> ...
>
> Now my question do I have to do anything or is GROMACS 5 taking care of the 
> correct termini in the AMBERE FF?
>

The information about manual prefixing is outdated, so we'll need to clean that 
up.  Bonds drawn in VMD are not definitive, but those in the topology are.  If 
you have multiple chains and the bonded structure in the topology is correct, 
then there's no problem.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] g_tune_pme_mpi is not compatible to mdrun_mpi

[Ebert Maximilian]

Hi,

This all sounds super interesting. However, is there anything I can do for now 
or do I need to just find the best combination by hand?

Thank you very much,

Max

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten 
Kutzner
Sent: Montag, 29. September 2014 19:23
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

On 29 Sep 2014, at 18:40, Mark Abraham  wrote:

> Hi,
> 
> That seems suitable.
> 
Oh, it just occurred to me that on systems that use the Load Leveler, we have 
no means of specifying the number of MPI ranks on the command line, since 'poe' 
has no switch for that. 
So at least for this case I guess we also need to make the test optional.

Carsten

> 
> Mark
> 
> On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner  wrote:
> 
>> Hi,
>> 
>> On 29 Sep 2014, at 18:17, Mark Abraham  wrote:
>> 
>>> Hi,
>>> 
>>> It can't be fixed, because there is no surefire way to run an 
>>> arbitrary
>> tpr
>>> on arbitrary number of ranks, regardless of how you guess -npme 
>>> might succeed.
>> What about making this check on two ranks always, regardless of what 
>> was specified on the g_tune_pme command line? On two ranks, we will 
>> never have separate PME ranks, so it should always work, since we end 
>> up with two ranks, doing PP and then PME.
>> If the system is so small that you can not decompose it in two DD 
>> domains, there is no use to do tuning anyway.
>> 
>> So even if you say
>> g_tune_pme -np 48 -s input.tpr
>> 
>> we first check with
>> mpirun -np 2 mdrun -s input.tpr
>> 
>> and only after that continue with -np 48.
>> 
>> Carsten
>> 
>>> We should just make the check optional, instead of being a deal 
>>> breaker.
>>> 
>>> Mark
>>> On Sep 29, 2014 4:35 PM, "Carsten Kutzner"  wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I see where the problem is.
>>>> There is an initial check in g_tune_pme to make sure that parallel 
>>>> runs can be executed at all. This is being run with the automatic 
>>>> number of PME-only ranks, which is 11 for your input file.
>>>> Unfortunately, this results in 37 PP ranks, for which no domain 
>>>> decomposition can be found.
>>>> 
>>>> At some point in the past we discussed that this could happen and 
>>>> it should be fixed. Will open a bug entry.
>>>> 
>>>> Thanks,
>>>> Carsten
>>>> 
>>>> 
>>>> On 29 Sep 2014, at 15:36, Ebert Maximilian 
>> wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> this ist he command:
>>>>> 
>>>>> setenv MDRUN mdrun_mpi
>>>>> 
>>>>> g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch
>>>>> 
>>>>> 
>>>>> Here the output of perf.out
>>>>> 
>>>>> 
>>>>> 
>>>>>P E R F O R M A N C E   R E S U L T S
>>>>> 
>>>>> 
>>>>> g_tune_pme_mpi for Gromacs VERSION 5.0.1
>>>>> Number of ranks : 48
>>>>> The mpirun command is   : mpirun
>>>>> Passing # of ranks via  : -np
>>>>> The mdrun  command is   : mdrun_mpi
>>>>> mdrun args benchmarks   : -resetstep 100 -o bench.trr -x bench.xtc -cpo
>>>> bench.cpt -c bench.gro -e bench.edr -g bench.log
>>>>> Benchmark steps : 1000
>>>>> dlb equilibration steps : 100
>>>>> mdrun args at launchtime:
>>>>> Repeats for each test   : 2
>>>>> Input file  : ../eq_nvt/1ZG4_nvt.tpr
>>>>> PME/PP load estimate : 0.151964
>>>>> Number of particles  : 39489
>>>>> Coulomb type : PME
>>>>> Grid spacing x y z   : 0.114561 0.114561 0.114561
>>>>> Van der Waals type   : Cut-off
>>>>> 
>>>>> Will try these real/reciprocal workload settings:
>>>>> No.   scaling  rcoulomb  nkx  nky  nkz   spacing  rvdw  tpr file
>>>>> 0  1.00  1.20   72   72   72  0.12   1.20
>>>> ../eq_nvt/1ZG4_nvt_bench00.tpr
>>>>> 1  1.10  1.32   64   64   64  0.

[gmx-users] Working on a GPU cluster with GROMACS 5

[Ebert Maximilian]

Dear list,

I am benchmarking my system on a GPU cluster with 6 GPU’s and two quad core 
CPUs for each node. First I am wondering if there is any output which confirms 
how many CPUs and GPUs were used during the run? I find the output for GPUs in 
the log file but only for a single node. When I use multiple nodes why don’t 
the other nodes show up in the log file as hosts? For instance in this example 
I used two nodes and claimed 4 GPUs each but got this in my log file:

6 GPUs detected on host ngpu-a4-01:
  #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible

4 GPUs auto-selected for this run.
Mapping of GPUs to the 4 PP ranks in this node: #0, #1, #2, #3



ngpu-a4-02 is not shown here. Any idea? The job was submitted in the following 
way:

qsub -q @test -lnodes=2:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu

and the gromacs_run_gpu file:

#!/bin/csh
#

#PBS -o result_run10ns96-8.dat
#PBS -j oe
#PBS -W umask=022
#PBS -r n

cd 8_gpu

module add CUDA
module load gromacs/5.0.1-gpu

mpirun gmx_mpi mdrun -v -x -deffnm 10ns_rep1-8GPU


Another question I had was how can I define the number of CPUs and check if 
they were really used? I can’t find any information about the number of CPUs in 
the log file. I would also like to try combinations like 4 CPUs + 1 GPU or 2 
CPUs + 2 GPU. How do I set this up?

Thank you very much for your help,

Max

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Re: [gmx-users] Working on a GPU cluster with GROMACS 5

[Ebert Maximilian]

Hi Carsten,

thanks for your answer. I tried what you described and it is basically working 
except for letting multiple MPI workers use one GPU. In my setup I use 4 GPUs 
with 8 MPI workers and hence 8 CPUs and OpenMP 1.  This is how I start GROMACS:

mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s 
../run1ns.tpr

and I submit this using:

qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu

Now I get the following errors (the output is longer but to keep it shorter I 
omitted the rest):

Using 8 MPI processes
Using 1 OpenMP thread per MPI process

7 GPUs detected on host ngpu-a4-06:
  #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible
  #6: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: compatible

4 GPUs user-selected for this run.
Mapping of GPUs to the 8 PP ranks in this node: #0, #0, #1, #1, #2, #2, #3, #3

NOTE: You assigned GPUs to multiple MPI processes.

---
Program gmx_mpi, VERSION 5.0.1
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu,
 line: 61

Fatal error:
cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or 
unavailable

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

Error on rank 1, will try to stop all ranks
Halting parallel program gmx_mpi on CPU 1 out of 8

---
Program gmx_mpi, VERSION 5.0.1
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu,
 line: 61

Fatal error:
cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or 
unavailable

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

Error on rank 3, will try to stop all ranks
Halting parallel program gmx_mpi on CPU 3 out of 8

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Carsten Kutzner
Gesendet: Donnerstag, 18. Dezember 2014 17:27
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Max,

On 18 Dec 2014, at 15:30, Ebert Maximilian  wrote:

> Dear list,
> 
> I am benchmarking my system on a GPU cluster with 6 GPU's and two quad core 
> CPUs for each node. First I am wondering if there is any output which 
> confirms how many CPUs and GPUs were used during the run? I find the output 
> for GPUs in the log file but only for a single node. When I use multiple 
> nodes why don't the other nodes show up in the log file as hosts? For 
> instance in this example I used two nodes and claimed 4 GPUs each but got 
> this in my log file:
> 
> 6 GPUs detected on host ngpu-a4-01:
>  #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
> 
> 4 GPUs auto-selected for this run.
> Mapping of GPUs to the 4 PP ranks in this node: #0, #1, #2, #3
This will be the same across all nodes. Gromacs will refuse to run if there are 
not enough GPUs on any of your other nodes.

> 
> 
> 
> ngpu-a4-02 is not shown here. Any idea? The job was submitted in the 
> following way:
> 
> qsub -q @test -lnodes=2:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu
> 
> and the gromacs_run_gpu file:
> 
> #!/bin/csh
> #
> 
> #PBS -o result_run10ns96-8.dat
> #PBS -j oe
> #PBS -W umask=022
> #PBS -r n
> 
> cd 8_gpu
> 
> module add CUDA
> module load gromacs/5.0.1-gpu
> 
> mpirun gmx_mpi mdrun -v -x -deffnm 10ns_rep1-8GPU
> 
> 
> Another question I had was how can I define the number of CPUs and check if 
> they were really used?
Use -ntomp to control how many OpenMP threads each of your MPI processes will 
have.
This way you can make use of all cores you have on each nod

Re: [gmx-users] Working on a GPU cluster with GROMACS 5

[Ebert Maximilian]

Hi Carsten,

thanks again for your reply. The why our cluster is setup is that you ask for 
GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule 
out the possibility that someone is actually using the note I called for 7 GPUs 
(so the entire note) but with GPU id just assign the first 4 to GROMACS. I 
still get the same error. I also tried -gpu_id 00 or -gpu_id  to change the 
CPU and to only use a single GPU but I always get:

NOTE: You assigned GPUs to multiple MPI processes.

---
Program gmx_mpi, VERSION 5.0.1
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu,
 line: 61

Fatal error:
cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or 
unavailable

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

Error on rank 1, will try to stop all ranks
Halting parallel program gmx_mpi on CPU 1 out of 4

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Carsten Kutzner
Gesendet: Mittwoch, 7. Januar 2015 14:13
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Max,

On 07 Jan 2015, at 11:36, Ebert Maximilian  wrote:

> Hi Carsten,
> 
> thanks for your answer. I tried what you described and it is basically 
> working except for letting multiple MPI workers use one GPU. In my setup I 
> use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1.  This is how I 
> start GROMACS:
> 
> mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s 
> ../run1ns.tpr
> 
> and I submit this using:
> 
> qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu
why are you using ppn=4? Shouldn't that be 8?

> 
> Now I get the following errors (the output is longer but to keep it shorter I 
> omitted the rest):
> 
> Using 8 MPI processes
> Using 1 OpenMP thread per MPI process
> 
> 7 GPUs detected on host ngpu-a4-06:
>  #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
>  #6: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat: 
> compatible
> 
> 4 GPUs user-selected for this run.
> Mapping of GPUs to the 8 PP ranks in this node: #0, #0, #1, #1, #2, 
> #2, #3, #3
> 
> NOTE: You assigned GPUs to multiple MPI processes.
> 
> ---
> Program gmx_mpi, VERSION 5.0.1
> Source code file: 
> /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_too
> ls/pmalloc_cuda.cu, line: 61
> 
> Fatal error:
> cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are 
> busy or unavailable
> 
Could it be that someone else's processes are running on that node while 
Gromacs tries to use the GPUs? Maybe try to the the whole node, maybe even in 
interactive mode to play around.

Carsten

> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Error on rank 1, will try to stop all ranks Halting parallel program 
> gmx_mpi on CPU 1 out of 8
> 
> ---
> Program gmx_mpi, VERSION 5.0.1
> Source code file: 
> /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_too
> ls/pmalloc_cuda.cu, line: 61
> 
> Fatal error:
> cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are 
> busy or unavailable
> 
> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Error on rank 3, will try to stop all ranks Halting parallel program 
> gmx_mpi on CPU 3 out of 8
> 
> -Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag 
> von Carsten Kutzner
> Gesendet: Donnerstag, 18. Dezember 2014 17:27
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5
> 
>

Re: [gmx-users] Working on a GPU cluster with GROMACS 5

[Ebert Maximilian]

Hi Jiri,

Yes this seems to be the problem. Thank you very much. The GPUs on this cluster 
are in the exclusive thread mode. I will ask the administrator if we can change 
this.

Thank you very much!

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Jiri 
Kraus
Gesendet: Mittwoch, 7. Januar 2015 14:58
An: gromacs.org_gmx-users@maillist.sys.kth.se
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Max,

In which compute mode are the GPUs running? Do be able to share a GPU between 
multiple MPI ranks you either need to use the multi process service (MPS see: 
[1]) or let the GPUs run in default compute mode (see [2]). You can query the 
compute mode with nvidia-smi -q -d COMPUTE (see example output below) and 
change it with nvidia-smi -c DEFAULT. Changing the compute mode requires root.

Hope this helps

Jiri

[1] https://docs.nvidia.com/deploy/pdf/CUDA_Multi_Process_Service_Overview.pdf
[2] 
http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#compute-modes 

Example output of nvidia-smi -q -d COMPUTE:
==NVSMI LOG==

Timestamp   : Wed Jan  7 05:51:31 2015
Driver Version  : 340.32

Attached GPUs   : 6
GPU :04:00.0
Compute Mode: Default

GPU :05:00.0
Compute Mode: Default

GPU :08:00.0
Compute Mode: Default

GPU :09:00.0
Compute Mode: Default

GPU :83:00.0
Compute Mode: Default

GPU :84:00.0
Compute Mode: Default

> Message: 5
> Date: Wed, 7 Jan 2015 13:42:46 +
> From: Ebert Maximilian 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] Working on a GPU cluster with GROMACS 5
> Message-ID:
>cour.sim.umontreal.ca>
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Carsten,
> 
> thanks again for your reply. The why our cluster is setup is that you 
> ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 
> there. But to rule out the possibility that someone is actually using 
> the note I called for 7 GPUs (so the entire note) but with GPU id just assign 
> the first 4 to GROMACS.
> I still get the same error. I also tried -gpu_id 00 or -gpu_id  to 
> change the CPU and to only use a single GPU but I always get:
> 
> NOTE: You assigned GPUs to multiple MPI processes.
> 
> ---
> Program gmx_mpi, VERSION 5.0.1
> Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-
> 5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61
> 
> Fatal error:
> cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are 
> busy or unavailable
> 
> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Error on rank 1, will try to stop all ranks Halting parallel program 
> gmx_mpi on CPU 1 out of 4
> 
> -Urspr?ngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag 
> von Carsten Kutzner
> Gesendet: Mittwoch, 7. Januar 2015 14:13
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5
> 
> Hi Max,
> 
> On 07 Jan 2015, at 11:36, Ebert Maximilian  wrote:
> 
> > Hi Carsten,
> >
> > thanks for your answer. I tried what you described and it is 
> > basically
> working except for letting multiple MPI workers use one GPU. In my 
> setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1.  
> This is how I start GROMACS:
> >
> > mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s 
> > ../run1ns.tpr
> >
> > and I submit this using:
> >
> > qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu
> why are you using ppn=4? Shouldn't that be 8?
> 
> >
> > Now I get the following errors (the output is longer but to keep it 
> > shorter I
> omitted the rest):
> >
> > Using 8 MPI processes
> > Using 1 OpenMP thread per MPI process
> >
> > 7 GPUs detected on host ngpu-a4-06:
> >  #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat:
> > compatible
> >  #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat:
> > compatible
> >  #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, stat:
> > compatible
> >  #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC:  no, s

Re: [gmx-users] Working on a GPU cluster with GROMACS 5

[Ebert Maximilian]

I just thought we might add this information to the 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization page. 
Could be useful for every user of a managed cluster. Usually you never come 
across this type of knowledge as a user.

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Ebert 
Maximilian
Gesendet: Mittwoch, 7. Januar 2015 15:07
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Jiri,

Yes this seems to be the problem. Thank you very much. The GPUs on this cluster 
are in the exclusive thread mode. I will ask the administrator if we can change 
this.

Thank you very much!

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Jiri 
Kraus
Gesendet: Mittwoch, 7. Januar 2015 14:58
An: gromacs.org_gmx-users@maillist.sys.kth.se
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Max,

In which compute mode are the GPUs running? Do be able to share a GPU between 
multiple MPI ranks you either need to use the multi process service (MPS see: 
[1]) or let the GPUs run in default compute mode (see [2]). You can query the 
compute mode with nvidia-smi -q -d COMPUTE (see example output below) and 
change it with nvidia-smi -c DEFAULT. Changing the compute mode requires root.

Hope this helps

Jiri

[1] https://docs.nvidia.com/deploy/pdf/CUDA_Multi_Process_Service_Overview.pdf
[2] 
http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#compute-modes 

Example output of nvidia-smi -q -d COMPUTE:
==NVSMI LOG==

Timestamp   : Wed Jan  7 05:51:31 2015
Driver Version  : 340.32

Attached GPUs   : 6
GPU :04:00.0
Compute Mode: Default

GPU :05:00.0
Compute Mode: Default

GPU :08:00.0
Compute Mode: Default

GPU :09:00.0
Compute Mode: Default

GPU :83:00.0
Compute Mode: Default

GPU :84:00.0
Compute Mode: Default

> Message: 5
> Date: Wed, 7 Jan 2015 13:42:46 +
> From: Ebert Maximilian 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] Working on a GPU cluster with GROMACS 5
> Message-ID:
>cour.sim.umontreal.ca>
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Carsten,
> 
> thanks again for your reply. The why our cluster is setup is that you 
> ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 
> there. But to rule out the possibility that someone is actually using 
> the note I called for 7 GPUs (so the entire note) but with GPU id just assign 
> the first 4 to GROMACS.
> I still get the same error. I also tried -gpu_id 00 or -gpu_id  to 
> change the CPU and to only use a single GPU but I always get:
> 
> NOTE: You assigned GPUs to multiple MPI processes.
> 
> ---
> Program gmx_mpi, VERSION 5.0.1
> Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-
> 5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61
> 
> Fatal error:
> cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are 
> busy or unavailable
> 
> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Error on rank 1, will try to stop all ranks Halting parallel program 
> gmx_mpi on CPU 1 out of 4
> 
> -Urspr?ngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag 
> von Carsten Kutzner
> Gesendet: Mittwoch, 7. Januar 2015 14:13
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5
> 
> Hi Max,
> 
> On 07 Jan 2015, at 11:36, Ebert Maximilian  wrote:
> 
> > Hi Carsten,
> >
> > thanks for your answer. I tried what you described and it is 
> > basically
> working except for letting multiple MPI workers use one GPU. In my 
> setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1.
> This is how I start GROMACS:
> >
> > mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s 
> > ../run1ns.tpr
> >
> > and I submit this using:
> >
> > qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu
> why are you using ppn=4? Shouldn't that be 8?
> 
> >
> > Now I get the following errors (the output is l

[gmx-users] g_tune_pme_mpi on GPU cluster fails

[Ebert Maximilian]

Hi there,

I have again a question regarding our GPU cluster. I tried to g_tune_pme_mpi on 
the cluster. After starting it across 3 nodes I get the following errors:


Command line:
  g_tune_pme_mpi -v -x -deffnm 1G68_run1ns -s ../run100ns.tpr

Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision)
Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision)
Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision)
Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision)
Will test 1 tpr file.
Will test 1 tpr file.
Will test 1 tpr file.
Will test 1 tpr file.
[ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be 
sent to a process whose contact information is unknown in file rml_oob_send.c 
at line 104
[ngpu-a4-06:13382] [[25869,1],0] could not get route to [[INVALID],INVALID]
[ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be 
sent to a process whose contact information is unknown in file 
base/plm_base_proxy.c at line 81
[ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be 
sent to a process whose contact information is unknown in file rml_oob_send.c 
at line 104
[ngpu-a4-06:13385] [[25869,1],1] could not get route to [[INVALID],INVALID]
[ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be 
sent to a process whose contact information is unknown in file 
base/plm_base_proxy.c at line 81
[ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be 
sent to a process whose contact information is unknown in file rml_oob_send.c 
at line 104
[ngpu-a4-06:13384] [[25869,1],2] could not get route to [[INVALID],INVALID]
[ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be 
sent to a process whose contact information is unknown in file 
base/plm_base_proxy.c at line 81
.
=>> PBS: job killed: walltime 3641 exceeded limit 3600
mpirun: killing job...

[ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],3] mca_oob_tcp_msg_recv: readv 
failed: Connection reset by peer (104)
[ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],2] mca_oob_tcp_msg_recv: readv 
failed: Connection reset by peer (104)
[ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],0] mca_oob_tcp_msg_recv: readv 
failed: Connection reset by peer (104)
[ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],1] mca_oob_tcp_msg_recv: readv 
failed: Connection reset by peer (104)


Any idea what is wrong?

Thank you very much!

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Ebert 
Maximilian
Gesendet: Mittwoch, 7. Januar 2015 14:43
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Carsten,

thanks again for your reply. The why our cluster is setup is that you ask for 
GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule 
out the possibility that someone is actually using the note I called for 7 GPUs 
(so the entire note) but with GPU id just assign the first 4 to GROMACS. I 
still get the same error. I also tried -gpu_id 00 or -gpu_id  to change the 
CPU and to only use a single GPU but I always get:

NOTE: You assigned GPUs to multiple MPI processes.

---
Program gmx_mpi, VERSION 5.0.1
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu,
 line: 61

Fatal error:
cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or 
unavailable

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

Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on 
CPU 1 out of 4

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Carsten Kutzner
Gesendet: Mittwoch, 7. Januar 2015 14:13
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5

Hi Max,

On 07 Jan 2015, at 11:36, Ebert Maximilian  wrote:

> Hi Carsten,
> 
> thanks for your answer. I tried what you described and it is basically 
> working except for letting multiple MPI workers use one GPU. In my setup I 
> use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1.  This is how I 
> start GROMACS:
> 
> mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s 
> ../run1ns.tpr
> 
> and I submit this using:
> 
> qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu
why are you using ppn=4? Shouldn't that be 8?

> 
> Now I get the following errors (the output is longer but to keep it shorter I 
> omitted the rest):
> 
> Using 8 MPI processes
> Using 1 OpenMP thread per MPI proces

[gmx-users] Log output of GPU accelerated GROMACS

[Ebert Maximilian]

Dear list,

I was wondering why the log file does not always contains the same information. 
In one of my configurations I got the following information:

GPU timings
-
 Computing: Count  Wall t (s)  ms/step   %
-
 Pair list H2D   1251   0.5630.450 0.2
 X / q H2D  50001   6.9980.140 2.9
 Nonbonded F kernel 47500 212.1184.46686.7
 Nonbonded F+ene k.  1250   9.3717.497 3.8
 Nonbonded F+ene+prune k.1251   9.7597.801 4.0
 F D2H  50001   5.8740.117 2.4
-
 Total244.6834.894   100.0
-

Force evaluation time GPU/CPU: 4.894 ms/4.012 ms = 1.220
For optimal performance this ratio should be close to 1!

But I never got this information in any other configuration using GPUs. Is this 
only part of the output if there is a problem with too much work for the GPU?

Thank you very much,

Max
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Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails

[Ebert Maximilian]

Hi Carsten,

I was benchmarking my first system and I do not see any improvement in using 
more than one GPU node. In the end I think having a node dedicated as PME node 
would make sense after all since our GPU cluster only consists of 9 nodes. What 
do you mean with high parallelization? What do you consider high?

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Carsten Kutzner
Gesendet: Mittwoch, 7. Januar 2015 17:04
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails

Hi,

there are two issues here:

a) you must not start multiple copies of g_tune_pme, but a single one.
g_tune_pme will by itself launch MPI-parallel mdrun processes (the path to the 
mdrun executable needs to be specified in the MDRUN environment variable, you 
might need to set others as well depending on your queueing system - read 
g_tune_pme -h.

b) g_tune_pme can not (yet) automatically deal with GPU nodes. With GPUs, 
separate PME nodes will also only make sense at very high parallelization - how 
many of these nodes do you want to use in parallel?

Carsten


On 07 Jan 2015, at 15:11, Ebert Maximilian  wrote:

> Hi there,
> 
> I have again a question regarding our GPU cluster. I tried to g_tune_pme_mpi 
> on the cluster. After starting it across 3 nodes I get the following errors:
> 
> 
> Command line:
>  g_tune_pme_mpi -v -x -deffnm 1G68_run1ns -s ../run100ns.tpr
> 
> Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading 
> file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file 
> ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file 
> ../run100ns.tpr, VERSION 5.0.1 (single precision) Will test 1 tpr 
> file.
> Will test 1 tpr file.
> Will test 1 tpr file.
> Will test 1 tpr file.
> [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is 
> attempting to be sent to a process whose contact information is 
> unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13382] 
> [[25869,1],0] could not get route to [[INVALID],INVALID] 
> [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is 
> attempting to be sent to a process whose contact information is 
> unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13385] 
> [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a 
> process whose contact information is unknown in file rml_oob_send.c at 
> line 104 [ngpu-a4-06:13385] [[25869,1],1] could not get route to 
> [[INVALID],INVALID] [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A 
> message is attempting to be sent to a process whose contact information is 
> unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13384] 
> [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process 
> whose contact information is unknown in file rml_oob_send.c at line 104 
> [ngpu-a4-06:13384] [[25869,1],2] could not get route to [[INVALID],INVALID] 
> [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to 
> be sent to a process whose contact information is unknown in file 
> base/plm_base_proxy.c at line 81 .
> =>> PBS: job killed: walltime 3641 exceeded limit 3600
> mpirun: killing job...
> 
> [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],3] mca_oob_tcp_msg_recv: 
> readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] 
> [[25869,0],0]-[[25869,1],2] mca_oob_tcp_msg_recv: readv failed: 
> Connection reset by peer (104) [ngpu-a4-06:13356] 
> [[25869,0],0]-[[25869,1],0] mca_oob_tcp_msg_recv: readv failed: 
> Connection reset by peer (104) [ngpu-a4-06:13356] 
> [[25869,0],0]-[[25869,1],1] mca_oob_tcp_msg_recv: readv failed: 
> Connection reset by peer (104)
> 
> 
> Any idea what is wrong?
> 
> Thank you very much!
> 
> Max
> 
> -----Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag 
> von Ebert Maximilian
> Gesendet: Mittwoch, 7. Januar 2015 14:43
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5
> 
> Hi Carsten,
> 
> thanks again for your reply. The why our cluster is setup is that you ask for 
> GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to 
> rule out the possibility that someone is actually using the note I called for 
> 7 GPUs (so the entire note) but with GPU id just assign the first 4 to 
> GROMACS. I still get the same error. I also tried -gpu_id 00 or -gpu_id  
> to change the CPU and to only use a single GPU but I always get:
> 
> NOTE: You assigned GPUs to multiple MPI processes.
> 
> ---
&g

[gmx-users] Performance difference between MPI ranks and OpenMP

[Ebert Maximilian]

Hi list,

I have another question regarding performance. Is there any performance 
difference if I start a process on a 8 CPU machine with 8 MPI ranks and 1 
OpenMP or 4 MPI ranks an 2 OpenMP? Both should use the 8 CPUs right?

Thank you very much,

Max
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Re: [gmx-users] Performance difference between MPI ranks and OpenMP

[Ebert Maximilian]

The reason I am asking is because I want to use two GPUs and 8 CPUs. So for now 
I have 2 MPI ranks and 4 OpenMP threads. Is there a way to have 8 MPI ranks but 
only use 2 GPUs? I also tried 8 MPI ranks with -gpu_id  but it was 
about the same as 2 MPI ranks with 4 OpenMP.

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Carsten Kutzner
Gesendet: Donnerstag, 8. Januar 2015 15:48
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Performance difference between MPI ranks and OpenMP


On 08 Jan 2015, at 15:38, Ebert Maximilian  wrote:

> Hi list,
> 
> I have another question regarding performance. Is there any performance 
> difference if I start a process on a 8 CPU machine with 8 MPI ranks and 1 
> OpenMP or 4 MPI ranks an 2 OpenMP? Both should use the 8 CPUs right?
Right, but there is a performance difference (try it out! :) Normally using 
just one layer of parallelization is fastest (less overhead), i.e.
using just OpenMP threads or just MPI ranks. However, more than 8 or so OpenMP 
threads per rank seldom yield optimal performance, so that a hybrid 
parallelization approach makes sense in such situations.

Carsten


> 
> Thank you very much,
> 
> Max
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry Theoretical and Computational 
Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: 
+49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails

[Ebert Maximilian]

I always read this few hundred atoms per core. But how is this in the context 
of a GPU? For instance we use the GTX580 with 512 cores. Do they count as 
cores? Because the system I am working on has 13,000 atoms. With 8 CPU cores 
and 2 GPUs (with a total of 1024 cores) how do I count this? Do I have 1032 
cores for 13,000 atoms? Do I count them individually? 13,000/8 and 13,000/1024? 
So that if I would have more CPUs per node I could achieve better performance?

Max

-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Carsten Kutzner
Gesendet: Donnerstag, 8. Januar 2015 15:51
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails


On 08 Jan 2015, at 15:32, Ebert Maximilian  wrote:

> Hi Carsten,
> 
> I was benchmarking my first system and I do not see any improvement in using 
> more than one GPU node.
Whether you see an improvement or not depends on the size of your system and 
the latency of your interconnect. If it is Gigabit Ethernet, it might be the 
bottleneck.

> In the end I think having a node dedicated as PME node would make sense after 
> all since our GPU cluster only consists of 9 nodes. What do you mean with 
> high parallelization? What do you consider high?
If you have so many cores that you end up with just a few hundred atoms per 
core I would say.

Carsten

> 
> Max
> 
> -Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag 
> von Carsten Kutzner
> Gesendet: Mittwoch, 7. Januar 2015 17:04
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails
> 
> Hi,
> 
> there are two issues here:
> 
> a) you must not start multiple copies of g_tune_pme, but a single one.
> g_tune_pme will by itself launch MPI-parallel mdrun processes (the path to 
> the mdrun executable needs to be specified in the MDRUN environment variable, 
> you might need to set others as well depending on your queueing system - read 
> g_tune_pme -h.
> 
> b) g_tune_pme can not (yet) automatically deal with GPU nodes. With GPUs, 
> separate PME nodes will also only make sense at very high parallelization - 
> how many of these nodes do you want to use in parallel?
> 
> Carsten
> 
> 
> On 07 Jan 2015, at 15:11, Ebert Maximilian  wrote:
> 
>> Hi there,
>> 
>> I have again a question regarding our GPU cluster. I tried to g_tune_pme_mpi 
>> on the cluster. After starting it across 3 nodes I get the following errors:
>> 
>> 
>> Command line:
>> g_tune_pme_mpi -v -x -deffnm 1G68_run1ns -s ../run100ns.tpr
>> 
>> Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) 
>> Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) 
>> Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) 
>> Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Will 
>> test 1 tpr file.
>> Will test 1 tpr file.
>> Will test 1 tpr file.
>> Will test 1 tpr file.
>> [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is 
>> attempting to be sent to a process whose contact information is 
>> unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13382] 
>> [[25869,1],0] could not get route to [[INVALID],INVALID] 
>> [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is 
>> attempting to be sent to a process whose contact information is 
>> unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13385] 
>> [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a 
>> process whose contact information is unknown in file rml_oob_send.c 
>> at line 104 [ngpu-a4-06:13385] [[25869,1],1] could not get route to 
>> [[INVALID],INVALID] [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A 
>> message is attempting to be sent to a process whose contact information is 
>> unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13384] 
>> [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a 
>> process whose contact information is unknown in file rml_oob_send.c at line 
>> 104 [ngpu-a4-06:13384] [[25869,1],2] could not get route to 
>> [[INVALID],INVALID] [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A 
>> message is attempting to be sent to a process whose contact information is 
>> unknown in file base/plm_base_proxy.c at line 81 .
>> =>> PBS: job killed: walltime 3641 exceeded limit 3600
>> mpirun: killing job...
>> 
>> [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],3] mca_oob_tcp_msg_recv: 
>> readv failed: Connection reset by peer (104

[gmx-users] g_rotacf lag time

[Ebert Maximilian]

Dear list,

is there a way to define the lag time for the auto correlation function in 
g_rotacf?

Thank you very much,

Max
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[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9

[Ebert Maximilian]

Hi there,

I have one question regarding the cosine content of an eigenvector. I did a PCA 
and calculated the cosine content of the 10 main eigenvectors. Except for the 
first all are really low. However, the main eigenvector is still around 0.9 
after 100ns simulation. I am pretty sure my system is equilibrated. Do you have 
any idea what might happen?

Thank you very much,

Max
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Re: [gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9

[Ebert Maximilian]

Hi Tsjerk,

thanks for your reply. Can you explain this sentence again please:

Not having a full set of cosines with periods equal to half the pc index just 
means you're not simulating gas or liquid.

The simulation runs already for 500ns and I analyzed 100ns from 400 to 500ns. 
How can a simple protein system not be equilibrated yet?

Max

> On Jan 15, 2015, at 3:52 PM, Tsjerk Wassenaar  wrote:
> 
> Hi Max,
> 
> The cosine content is a rather nonsensical parameter.
> HOWEVER, having a cosine content with 1/2 period that high one ANY
> eigenvector is indicative of unidirectional motion (a.k.a. conformational
> change/drift). That cosine contents with other periods on other
> eigenvectors is low is meaningless. Not having a full set of cosines with
> periods equal to half the pc index just means you're not simulating gas or
> liquid.
> 
> In short, your system is not equilibrated.
> 
> Cheers,
> 
> Tsjerk
> 
> On Thu, Jan 15, 2015 at 3:43 PM, Ebert Maximilian 
> wrote:
> 
>> Hi there,
>> 
>> I have one question regarding the cosine content of an eigenvector. I did
>> a PCA and calculated the cosine content of the 10 main eigenvectors. Except
>> for the first all are really low. However, the main eigenvector is still
>> around 0.9 after 100ns simulation. I am pretty sure my system is
>> equilibrated. Do you have any idea what might happen?
>> 
>> Thank you very much,
>> 
>> Max
>> --
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>> * Please search the archive at
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
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