date:20171127

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

2017-11-27 Thread zaved

> Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Pdb2gmx melts molecules due to bad distances (GIANMARCO BARTALINI)
>2. Not enough memory. Failed to realloc (RAHUL SURESH)
>3. Re: pH dependent simulation (Justin Lemkul)
>4. Re: pH dependent simulation (Justin Lemkul)
>5. Re: Pdb files generated on Lincs warning (Justin Lemkul)
>6. Re: Fatal error in grompp (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Mon, 27 Nov 2017 12:04:04 +0100
> From: GIANMARCO BARTALINI 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Pdb2gmx melts molecules due to bad distances
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Hello guys, I produced a system "protein + lipid membrane" using the
> online
> tool CHARMM-GUI. Since I need to use the Amber force field, I added the
> Lipids17 force field inside Gromacs. The implementation should work fine,
> since the conversion of an equilibrated structure produces a nice and
> correct gro file. But when I try to convert the (not minimized) PDB file
> that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
> lipid molecules are melted together (due to their bad distances). If I use
> this structure for a minimization, the calculation stops due to bad
> energies. Do you know how to solve this issue?
> Thank you in advance,
>
> Gianmarco
>
>
> --
>
> Message: 2
> Date: Mon, 27 Nov 2017 17:47:36 +0530
> From: RAHUL SURESH 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Not enough memory. Failed to realloc
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Users
>
> I am trying to carryout protein-metal interaction using charmm36 ff.
> During
> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
> solv.gro"
> *i receive a error stating
>
>
>
>
>
>
>
>
> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
> atoms_->atom,atoms_->atom=0(called from
> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line
> 86)". *
> I have enough space to carry out this simulation and I am using 2016
> version of gromacs.
>
> I couldnt diagonise the error exactly. Any help on this will be of great
> use.
>
> Thank you
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
>
> --
>
> Message: 3
> Date: Mon, 27 Nov 2017 08:31:18 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] pH dependent simulation
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Thank you so much sir.
>
> On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote:
>> Hello Everyone
>>
>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>> positively charged residues.
>>
>> However upon predicting the pKa values using H++ server, I am getting
>> the
>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And
>> the
>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>> should have different pKa values at pH 7 and 9).
>
> Why do you expect that? There are no amino acids with pKa in that range,
> so nothing should change unless there are unique microenvironments that
> shift canonical pKa values. As H++ has not detected any, likely your
> protein behaves canonically. You can confirm your calculated pKa values
> with another method, like PROPKA, to be sure.
>
> -Justin
>
>> Whether I am in the right direction or doing something wrong!!!
>>
>> Can anyone kindly suggest me how to proceed further?
>>
>> Any suggestion is appreciated.
>>
>> Thank You
>> Zaved
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely
>> for the individual named. If you are not the named addressee you should
>> not disseminate, distribute or copy this e-mail. Please notify the
>> sender immediately by e-mail if you have received this e-mail in error
>> and destroy it from your system. Though considerable effort has been
>> made to deliver error free e-mail messages but it can not be guaranteed
>> to be secure or error-free as information could be interc

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

2017-11-27 Thread zaved

> Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>   gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
>   gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Pdb2gmx melts molecules due to bad distances (GIANMARCO BARTALINI)
>2. Not enough memory. Failed to realloc (RAHUL SURESH)
>3. Re: pH dependent simulation (Justin Lemkul)
>4. Re: pH dependent simulation (Justin Lemkul)
>5. Re: Pdb files generated on Lincs warning (Justin Lemkul)
>6. Re: Fatal error in grompp (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Mon, 27 Nov 2017 12:04:04 +0100
> From: GIANMARCO BARTALINI 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Pdb2gmx melts molecules due to bad distances
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Hello guys, I produced a system "protein + lipid membrane" using the
> online
> tool CHARMM-GUI. Since I need to use the Amber force field, I added the
> Lipids17 force field inside Gromacs. The implementation should work fine,
> since the conversion of an equilibrated structure produces a nice and
> correct gro file. But when I try to convert the (not minimized) PDB file
> that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
> lipid molecules are melted together (due to their bad distances). If I use
> this structure for a minimization, the calculation stops due to bad
> energies. Do you know how to solve this issue?
> Thank you in advance,
>
> Gianmarco
>
>
> --
>
> Message: 2
> Date: Mon, 27 Nov 2017 17:47:36 +0530
> From: RAHUL SURESH 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Not enough memory. Failed to realloc
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Users
>
> I am trying to carryout protein-metal interaction using charmm36 ff.
> During
> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
> solv.gro"
> *i receive a error stating
>
>
>
>
>
>
>
>
> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
> atoms_->atom,atoms_->atom=0(called from
> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line
> 86)". *
> I have enough space to carry out this simulation and I am using 2016
> version of gromacs.
>
> I couldnt diagonise the error exactly. Any help on this will be of great
> use.
>
> Thank you
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
>
> --
>
> Message: 3
> Date: Mon, 27 Nov 2017 08:31:18 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] pH dependent simulation
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> Thank you sir for the explanation.

> On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote:
>> Hello Everyone
>>
>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>> positively charged residues.
>>
>> However upon predicting the pKa values using H++ server, I am getting
>> the
>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And
>> the
>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>> should have different pKa values at pH 7 and 9).
>
> Why do you expect that? There are no amino acids with pKa in that range,
> so nothing should change unless there are unique microenvironments that
> shift canonical pKa values. As H++ has not detected any, likely your
> protein behaves canonically. You can confirm your calculated pKa values
> with another method, like PROPKA, to be sure.
>
> -Justin
>
>> Whether I am in the right direction or doing something wrong!!!
>>
>> Can anyone kindly suggest me how to proceed further?
>>
>> Any suggestion is appreciated.
>>
>> Thank You
>> Zaved
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely
>> for the individual named. If you are not the named addressee you should
>> not disseminate, distribute or copy this e-mail. Please notify the
>> sender immediately by e-mail if you have received this e-mail in error
>> and destroy it from your system. Though considerable effort has been
>> made to deliver error free e-mail messages but it can not be guaranteed
>> to be secure or error-free as information co

Re: [gmx-users] Umbrella sampling

2017-11-27 Thread rose rahmani

Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?

Best regards
Rose

On Sun, Nov 26, 2017 at 12:39 AM, Justin Lemkul  wrote:

>
>
> On 11/25/17 3:59 PM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 3:07 PM, rose rahmani wrote:
>>>
>>> Oh sorry this is .mdp file:

 DEFINE   = -DPOSRES

 What are you restraining? This seems counterproductive, and by default
>>>
 (unless you've hacked the topology), this is going to restrain your
 protein, which is definitely wrong.

>>> yes, protein.you mean i should remove it and don't restraint anything?
>>> and
>>> for npt(previous step) run too?
>>>
>>
> What is the purpose of a restraint? To prevent motion. What is your
> objective? To cause motion of your protein towards a surface. Does it make
> sense to restrain the protein during this process?
>
> Equilibration is a separate matter.
>
> integrator   = md
 dt   = 0.001
 nsteps   = 200
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 500
 nstenergy= 1000
 nstxtcout= 1000
 rlist= 1.5
 rcoulomb = 1.5
 rvdw = 1.2

 Again, I am suspicious of these cutoffs. What force field are you using?
>>>
>>> AMBER99
>>>
>>
> Then yes, those cutoffs are wrong. This is also a very old force field,
> and newer/better variants of it exist. Refer to the literature to find the
> right cutoffs for the parameter set you decide upon. This is not a trivial
> matter.
>
>
> coulombtype  = pme
>>>
 cutoff-scheme= group
 vdwtype  = Switch
 rvdw_switch  = 1.0
 pcoupl   = no
 gen-vel  = yes
 gen-temp = 0
 gen-seed = 173529
 constraints  = h-bonds
 pbc  = xy
 freezegrps   = WAL ZnS
 freezedim= Y Y Y Y Y Y
 energygrp-excl   = WAL WAL ZnO ZnO
 energygrps   = SOL WAL ZnO Protein NA CL
 nwall= 2
 wall-atomtype= C C
 wall-type= 9-3
 wall-density = 150 150
 wall-ewald-zfac  = 3
 ewald-geometry   = 3dc
 fourierspacing   = 0.12
 tcoupl   = v-rescale
 tc-grps  = System
 tau-t= 0.1
 ref-t= 300
 pull= yes
 pull_ngroups= 2
 pull_ncoords= 1
 pull_group1_name= ZnS
 pull_group2_name= Protein-H

 You can probably just use the whole protein here, though I doubt it
>>> makes
>>> much difference.
>>>
>>> pull_coord1_type= umbrella  ; harmonic biasing force
>>>
 pull_coord1_geometry= distance  ; simple distance increase
 pull_coord1_groups  = 1 2
 pull_coord1_dim = N N Y
 pull_coord1_rate= 0.001

 Here's your problem. With a positive pull rate, you are instructing
>>> mdrun
>>>
 to increase the COM distance between the protein and the ZnS surface. If
 you want them to come closer, you need a negative value here, to
 decrease
 the distance as a function of time. Of course, this all goes out the
 window
 if your protein is restrained, as suggested above.

>>>
>>> oh, i've got it.
>> you restrained chain B in tutorial but i shouldn't because ZnS is freezed?
>>
>
> No, I restrained a chain in my protein to mimic the stability of
> (physiologically) much larger systems. People typically fail to read my
> paper that is the basis of that tutorial, in which this concept is
> explained. Perhaps I need to add a bold, flashing warning that people
> should not be blindly following the method.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@grom

Re: [gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread RAHUL SURESH

Dear Justin

It worked. Actually by its own. I reconstructed the pdb and gave again.

Thank you so much for your time

On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH 
wrote:

> This error occur only for this particular pdb structure. The protein here
> is attached with a metal ion. The necessary changes are made to the
> charmm36 ff.
>
> Should be some error in my pdb?
>
> On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH 
> wrote:
>
>> Here i have added the report for the commands
>>
>>
>> Command line:
>>   *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
>>
>> Read 628 atoms
>> Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
>> No velocities found
>> system size :  3.716 91.693  1.702 (nm)
>> diameter: 91.698   (nm)
>> center  : -0.048  0.153  0.001 (nm)
>> box vectors :  3.715 91.693  1.702 (nm)
>> box angles  :  90.00  90.00  90.00 (degrees)
>> box volume  : 579.93   (nm^3)
>> shift   : 46.897 46.696 46.848 (nm)
>> new center  : 46.849 46.849 46.849 (nm)
>> new box vectors : 93.698 93.698 93.698 (nm)
>> new box angles  :  90.00  90.00  90.00 (degrees)
>> new box volume  :822615.31   (nm^3)
>>
>>
>> Command line:
>>   *gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*
>>
>> Reading solute configuration
>> GROup of MAchos and Cynical Suckers
>> Containing 628 atoms in 43 residues
>> Reading solvent configuration
>> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
>> Containing 648 atoms in 216 residues
>>
>> Initialising inter-atomic distances...
>>
>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>>  based on residue and atom names, since they could not be
>>  definitively assigned from the information in your input
>>  files. These guessed numbers might deviate from the mass
>>  and radius of the atom type. Please check the output
>>  files if necessary.
>>
>> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
>> from the source below. This means the results may be different
>> compared to previous GROMACS versions.
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> A. Bondi
>> van der Waals Volumes and Radii
>> J. Phys. Chem. 68 (1964) pp. 441-451
>>   --- Thank You ---  
>>
>> Generating solvent configuration
>> Will generate new solvent configuration of 51x51x51 boxes
>> Solvent box contains 83316213 atoms in 27772071 residues
>>
>> ---
>> Program: gmx solvate, version 2016.4
>>
>> Memory allocation failed:
>> std::bad_alloc
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 11/27/17 11:26 AM, RAHUL SURESH wrote:
>>>
 Hi



 *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*

>>>
>>> And how large is the resulting box? Are all the coordinates properly
>>> defined? What is the full screen output of gmx solvate up to the failure?
>>>
>>> -Justin
>>>
>>>
>>> I have used the above command to generate the box. Infact I have used
 this
 command before and I never got any error.

 Thank you

 On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul  wrote:


> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
>
> Dear Users
>>
>> I am trying to carryout protein-metal interaction using charmm36 ff.
>> During
>> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
>> solv.gro"
>> *i receive a error stating
>>
>>
>>
>>
>>
>>
>>
>>
>> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes
>> for
>> atoms_->atom,atoms_->atom=0(called from
>> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
>> topology/atomsbuilder.cpp,line
>> 86)". *
>> I have enough space to carry out this simulation and I am using 2016
>> version of gromacs.
>>
>> How large is your box? Are you sure you have set its size in nm, not
> A?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
>

Re: [gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread RAHUL SURESH

This error occur only for this particular pdb structure. The protein here
is attached with a metal ion. The necessary changes are made to the
charmm36 ff.

Should be some error in my pdb?

On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH 
wrote:

> Here i have added the report for the commands
>
>
> Command line:
>   *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
>
> Read 628 atoms
> Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
> No velocities found
> system size :  3.716 91.693  1.702 (nm)
> diameter: 91.698   (nm)
> center  : -0.048  0.153  0.001 (nm)
> box vectors :  3.715 91.693  1.702 (nm)
> box angles  :  90.00  90.00  90.00 (degrees)
> box volume  : 579.93   (nm^3)
> shift   : 46.897 46.696 46.848 (nm)
> new center  : 46.849 46.849 46.849 (nm)
> new box vectors : 93.698 93.698 93.698 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  :822615.31   (nm^3)
>
>
> Command line:
>   *gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*
>
> Reading solute configuration
> GROup of MAchos and Cynical Suckers
> Containing 628 atoms in 43 residues
> Reading solvent configuration
> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
> Containing 648 atoms in 216 residues
>
> Initialising inter-atomic distances...
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>  based on residue and atom names, since they could not be
>  definitively assigned from the information in your input
>  files. These guessed numbers might deviate from the mass
>  and radius of the atom type. Please check the output
>  files if necessary.
>
> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
> from the source below. This means the results may be different
> compared to previous GROMACS versions.
>
>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
> A. Bondi
> van der Waals Volumes and Radii
> J. Phys. Chem. 68 (1964) pp. 441-451
>   --- Thank You ---  
>
> Generating solvent configuration
> Will generate new solvent configuration of 51x51x51 boxes
> Solvent box contains 83316213 atoms in 27772071 residues
>
> ---
> Program: gmx solvate, version 2016.4
>
> Memory allocation failed:
> std::bad_alloc
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/27/17 11:26 AM, RAHUL SURESH wrote:
>>
>>> Hi
>>>
>>>
>>>
>>> *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
>>>
>>
>> And how large is the resulting box? Are all the coordinates properly
>> defined? What is the full screen output of gmx solvate up to the failure?
>>
>> -Justin
>>
>>
>> I have used the above command to generate the box. Infact I have used this
>>> command before and I never got any error.
>>>
>>> Thank you
>>>
>>> On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul  wrote:
>>>
>>>
 On 11/27/17 7:17 AM, RAHUL SURESH wrote:

 Dear Users
>
> I am trying to carryout protein-metal interaction using charmm36 ff.
> During
> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
> solv.gro"
> *i receive a error stating
>
>
>
>
>
>
>
>
> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
> atoms_->atom,atoms_->atom=0(called from
> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
> topology/atomsbuilder.cpp,line
> 86)". *
> I have enough space to carry out this simulation and I am using 2016
> version of gromacs.
>
> How large is your box? Are you sure you have set its size in nm, not A?

 -Justin

 --
 ==

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

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

 jalem...@vt.edu | (540) 231-3129
 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

 ==

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>>>
>>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA

Re: [gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread RAHUL SURESH

Here i have added the report for the commands


Command line:
  *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*

Read 628 atoms
Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
No velocities found
system size :  3.716 91.693  1.702 (nm)
diameter: 91.698   (nm)
center  : -0.048  0.153  0.001 (nm)
box vectors :  3.715 91.693  1.702 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  : 579.93   (nm^3)
shift   : 46.897 46.696 46.848 (nm)
new center  : 46.849 46.849 46.849 (nm)
new box vectors : 93.698 93.698 93.698 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :822615.31   (nm^3)


Command line:
  *gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*

Reading solute configuration
GROup of MAchos and Cynical Suckers
Containing 628 atoms in 43 residues
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues

Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
  --- Thank You ---  

Generating solvent configuration
Will generate new solvent configuration of 51x51x51 boxes
Solvent box contains 83316213 atoms in 27772071 residues

---
Program: gmx solvate, version 2016.4

Memory allocation failed:
std::bad_alloc

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


On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul  wrote:

>
>
> On 11/27/17 11:26 AM, RAHUL SURESH wrote:
>
>> Hi
>>
>>
>>
>> *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
>>
>
> And how large is the resulting box? Are all the coordinates properly
> defined? What is the full screen output of gmx solvate up to the failure?
>
> -Justin
>
>
> I have used the above command to generate the box. Infact I have used this
>> command before and I never got any error.
>>
>> Thank you
>>
>> On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
>>>
>>> Dear Users

 I am trying to carryout protein-metal interaction using charmm36 ff.
 During
 solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
 solv.gro"
 *i receive a error stating








 *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
 atoms_->atom,atoms_->atom=0(called from
 file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
 topology/atomsbuilder.cpp,line
 86)". *
 I have enough space to carry out this simulation and I am using 2016
 version of gromacs.

 How large is your box? Are you sure you have set its size in nm, not A?
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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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>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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Re: [gmx-users] Fatal error in grompp

2017-11-27 Thread Justin Lemkul




On 11/27/17 3:12 PM, Saumyak Mukherjee wrote:

Dear Justin,

Thanks for the reply.

In that case, if I want the SOL-Backbone interaction energy, how shall I
choose the energygrps? Is it possible to have such a group in the index.ndx
file?


You have to have fully intact charge groups, which means including H 
atoms and whatever else the force field characterizes as a full charge 
group. You might be able to define such a group, but the quantity that 
comes out of the calculation probably doesn't have any physical meaning.


-Justin


Regards,
Saumyak



‌

On 27 November 2017 at 19:05, Justin Lemkul  wrote:



On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:


Dear All,

I want to calculate the interaction energy between water and protein
backbone. However, in mdp file, when I am using

energygrps = SOL backbone

grompp is returning the following error.

Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
different energy groups

Can someone kindly point out my mistake?


You can't make the backbone a separate energy group. Look at what atoms 1
and 2 are - likely it's the N-terminal N and one H atom, which have to be
in the same group to do a group-based, pairwise energy decomposition.
Whatever groups you establish have to contain full charge groups.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Fatal error in grompp

2017-11-27 Thread Saumyak Mukherjee

Dear Justin,

Thanks for the reply.

In that case, if I want the SOL-Backbone interaction energy, how shall I
choose the energygrps? Is it possible to have such a group in the index.ndx
file?

Regards,
Saumyak



‌

On 27 November 2017 at 19:05, Justin Lemkul  wrote:

>
>
> On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:
>
>> Dear All,
>>
>> I want to calculate the interaction energy between water and protein
>> backbone. However, in mdp file, when I am using
>>
>> energygrps = SOL backbone
>>
>> grompp is returning the following error.
>>
>> Fatal error:
>> atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
>> different energy groups
>>
>> Can someone kindly point out my mistake?
>>
>
> You can't make the backbone a separate energy group. Look at what atoms 1
> and 2 are - likely it's the N-terminal N and one H atom, which have to be
> in the same group to do a group-based, pairwise energy decomposition.
> Whatever groups you establish have to contain full charge groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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-- 
Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.
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Re: [gmx-users] Build thin film.

2017-11-27 Thread ali akgün

Thank you :)

On Sun, Nov 26, 2017 at 11:36 PM, Dallas Warren 
wrote:

> You can do whatever you want, and there are many tools to help you do that.
>
> Couple of options are using gmx insert-molecules (constrain the box
> size to make the film, then enlarge afterwards to insert other
> molecules), gmx genconf (just stack as required, some initial care
> with runs will be required to get to correct size/density), or packmol
> (http://www.ime.unicamp.br/~martinez/packmol/home.shtml)
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 24 November 2017 at 03:51, ali akgün  wrote:
> > I have a pdb file can i build thin film  ?
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread Justin Lemkul




On 11/27/17 11:26 AM, RAHUL SURESH wrote:

Hi



*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*


And how large is the resulting box? Are all the coordinates properly 
defined? What is the full screen output of gmx solvate up to the failure?


-Justin


I have used the above command to generate the box. Infact I have used this
command before and I never got any error.

Thank you

On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul  wrote:



On 11/27/17 7:17 AM, RAHUL SURESH wrote:


Dear Users

I am trying to carryout protein-metal interaction using charmm36 ff.
During
solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
solv.gro"
*i receive a error stating








*"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
atoms_->atom,atoms_->atom=0(called from
file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
topology/atomsbuilder.cpp,line
86)". *
I have enough space to carry out this simulation and I am using 2016
version of gromacs.


How large is your box? Are you sure you have set its size in nm, not A?

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

2017-11-27 Thread David van der Spoel


On 26/11/17 17:08, Rakesh Pant wrote:

Dear Alex,

But g-x2top doesn't work till we define all atom types in .n2t file.


Please do not use this at all. Use acpype or something.


Thanks


On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin"  wrote:

Hi,

You will need to have both ffbonded.itp and ffnonbonded.itp .

atomname2type.n2t is needed for g_x2top to make it work correctly.

Good luck.


-Alex



On 26/11/2017 10:52, Rakesh Pant wrote:


Dear,  Alex
Does it mean, we do not need to define all the atomtypes in the .nt2 file.
It is enough to define all types in bonded and non-bonded itp.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin 
wrote:

Edit the content of you ffnonbonded.itp file approximately this way:


[ atomtypes ]
;nameat.nummasschargeptypesigma epsilon
C1412.001.08A0.440000.63  ;
OCE815.999400-0.70A0.354000.159705  ; C-O-C
Bridging Oxygen;
OCH815.999400-0.51A0.354000.159705  ; C-O-H
Oxygen;

HCO1 1.0080000.32A0.044900.235725  ; H-O-C
Hydrogen;


You would need to search literature for respective ff parameters: all the
above parameters are taken from another topology to give a template.


-Alex


On 26/11/2017 10:37, Rakesh Pant wrote:

Dear Alex,

If I use O atoms to define the respective functional groups, then how
to
include the C atoms present in the molecule.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 


wrote:

Hi,


As I understood the problem, you need to distinguish between surface and
buried carbons?

You could define two atomtypes that differ in name and use it to process
with x2top.

Below is an example of *.n2t lines. You would need to change the charges
and bondlengthes.

...

OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
group
OOCE-1.0515.99942C0.154 C 0.154; bridge
oxygen

...

Then you need *.n2t file in your ff.

Good luck!


-Alex


On 25/11/2017 22:06, Justin Lemkul wrote:


On 11/25/17 3:31 PM, Rakesh Pant wrote:


But then I how will include the C atom (which is also one of the


atomtypes)?

No idea, but I know people on this list have dealt with graphene oxide


before, so hopefully someone else chimes in.

-Justin


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Re: [gmx-users] Performance test

2017-11-27 Thread Javier Luque Di Salvo

Dear community,
I share the results of scaling- performance test. I used this command and
checked the core usage with the help of htop tool (http://hisham.hm/htop/):
gmx mdrun -ntmpi 1 -ntomp N -pin on -deffnm  &

Where N is the number of (logical) cores, and hardware is Intel(R) Core(TM)
i7-6700 @3.40 GHz, 16 GB RAM and no GPU. I tested two polymer chains of
different size (psu10= 552 atoms; psu36= 1956 atoms), 1ns NPT simulations
of the previously-equilibrated system, md settings were Berendsen
thermostat and barostat, V-rescale, time step 1fs, rcut-off 1.0 nm, PME for
coulombic computation. In this link the figures:
https://goo.gl/bVZKcU

And the table with the values if problems in opening the figures:
PSU10 (552 atoms)
N   wall-time  ns/day
1   1057.166   81.7025
2   631.117  136.908
3   461.265  187.448
4   352.821  244.886
5   440.070  196.393
6   386.782  223.346
7   348.273  248.083
8   389.243  255.187
--
PSU36 (1956 atoms)
N   wall-time  ns/day
1   2259.990  38.231
2   1254.619  68.870
3   875.394   99.267
4   672.042   128.570
5   822.385   105.056
6   712.061   121.338
7   628.172   137.551
8   576.145   149.963

Kind regards,
Javi

2017-11-21 13:50 GMT+01:00 Javier E :

> Dear users,
>
> I'm doing a performance analysis following this link
> http://manual.gromacs.org/documentation/5.1/user-guide/
> mdrun-performance.html and wanted to ask:
>
> Is there a "standard" procedure to test performance in gromacs (on single
> nodes, one multi-processor CPU)? Following there are some results, the
> system is a small polymeric chain of 542 atoms with no water and NPT 100 ps
> runs (if more information about md settings are needed please ask):
>
> Running on 1 node with total 4 cores, 8 logical cores
> Hardware detected:
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: AVX2_256
>
> GROMACS version: VERSION 5.1.4
> Precision:single
> Memory model:64 bit
> MPI library:  thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:   disabled
> OpenCL support:  disabled
>
>
> gmx mdrun -ntmpi 1 -ntomp # -v -deffnm out.tpr
>
>
> ___
> -ntomp  | MPI / OpenMP- | Wall time (s)|ns/day   |  % CPU   |
> Note?* |
> 
> -
>1|  1/1 | 1075.764  |80.315|
> 100.0   |   No   |
>2|  1/2 |  619.679   |   139.427   |
> 200.0   |   Yes |
>3|  1/3 |  458.721   |   188.350   |
> 299.9   |   Yes |
>4|  1/4 |  356.906   |   242.081   |
> 399.8   |   Yes |
>5|  1/5 |  433.572   |   199.275   |
> 499.0   |   Yes |
>6|  1/6 |  378.951   |   227.998   |
> 598.0   |   Yes |
>7|  1/7 |  355.785   |   242.844   |
> 693.1   |   Yes |
>8|  1/8 (default)|  328.520   |   262.081   |
> 779.0   |   No   |
> 
> -
>
> *NOTE: The number of threads is not equal to the number of (logical) cores
>   and the -pin option is set to auto: will not pin thread to cores.
>
>
> If (MPI-Threads)*(OpenMP-Threads) = number of threads, does mdrun uses
> number of cores= number of threads, and this can be seen in the %CPU usage?
>
> For example, as I installed GROMACS in default, the GMX_OpenMP_MAX_THREAD
> is set at 32 threads, but this will never happen with this hardware (4
> cores, 8 logical), is this correct? By now I'm re-running the exact same
> tests to have at least one replica, and extending the system size and the
> and run time. Any suggestions on how to deep further in this kind of tests
> are welcome,
>
> Best regards
> --
>
> 
>
> *Javier Luque Di Salvo*
>
> Dipartamento di Ingegneria Chimica
>
> Universitá Degli Studi di Palermo
> *Viale delle Scienze, Ed. 6*
> *90128 PALERMO (PA)*
> *+39.09123867503 <+39%20091%202386%207503>*
>



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Dipartamento di Ingegneria Chimica

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Re: [gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread RAHUL SURESH

Hi



*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
I have used the above command to generate the box. Infact I have used this
command before and I never got any error.

Thank you

On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul  wrote:

>
>
> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
>
>> Dear Users
>>
>> I am trying to carryout protein-metal interaction using charmm36 ff.
>> During
>> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
>> solv.gro"
>> *i receive a error stating
>>
>>
>>
>>
>>
>>
>>
>>
>> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
>> atoms_->atom,atoms_->atom=0(called from
>> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
>> topology/atomsbuilder.cpp,line
>> 86)". *
>> I have enough space to carry out this simulation and I am using 2016
>> version of gromacs.
>>
>
> How large is your box? Are you sure you have set its size in nm, not A?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] pH dependent simulation

2017-11-27 Thread Tasneem Kausar

Thanks for correcting..

On Mon, Nov 27, 2017 at 7:02 PM, Justin Lemkul  wrote:

>
>
> On 11/27/17 1:02 AM, Tasneem Kausar wrote:
>
>> pKa of amino acid residue is a constant quantity. Depending on the pH you
>>
>
> That's not strictly true. Titratable amino acids can be found in unique
> microenvironments that cause shifts in canonical values. For instance,
> there are some catalytic lysines known in hydrophobic environments that
> have pKa values of ~4 instead of the canonical value of ~10.5.
>
> -Justin
>
> can protonate and deprotonate amino acid according to the pKa of particular
>> residue.
>>
>> > =link&utm_campaign=sig-email&utm_content=webmail>
>> Virus-free.
>> www.avast.com
>> > =link&utm_campaign=sig-email&utm_content=webmail>
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>>
>> On Mon, Nov 27, 2017 at 9:39 AM,  wrote:
>>
>> Hello Everyone
>>>
>>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>>> positively charged residues.
>>>
>>> However upon predicting the pKa values using H++ server, I am getting the
>>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And
>>> the
>>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>>> should have different pKa values at pH 7 and 9).
>>>
>>> Whether I am in the right direction or doing something wrong!!!
>>>
>>> Can anyone kindly suggest me how to proceed further?
>>>
>>> Any suggestion is appreciated.
>>>
>>> Thank You
>>> Zaved
>>>
>>>
>>> * * * D I S C L A I M E R * * *
>>> This e-mail may contain privileged information and is intended solely for
>>> the individual named. If you are not the named addressee you should not
>>> disseminate, distribute or copy this e-mail. Please notify the sender
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>>> error free e-mail messages but it can not be guaranteed to be secure or
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>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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[gmx-users] SPC/Fw model of water

2017-11-27 Thread Iman Ahmadabadi

Dear Gromacs Users,

I need the SPC/Fw model of water. Could I receive this model?

Best Regards
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Re: [gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread Justin Lemkul




On 11/27/17 7:17 AM, RAHUL SURESH wrote:

Dear Users

I am trying to carryout protein-metal interaction using charmm36 ff. During
solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro"
*i receive a error stating








*"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
atoms_->atom,atoms_->atom=0(called from
file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line
86)". *
I have enough space to carry out this simulation and I am using 2016
version of gromacs.


How large is your box? Are you sure you have set its size in nm, not A?

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

2017-11-27 Thread Justin Lemkul




On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:

Hello guys, I produced a system "protein + lipid membrane" using the online
tool CHARMM-GUI. Since I need to use the Amber force field, I added the
Lipids17 force field inside Gromacs. The implementation should work fine,
since the conversion of an equilibrated structure produces a nice and
correct gro file. But when I try to convert the (not minimized) PDB file
that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
lipid molecules are melted together (due to their bad distances). If I use
this structure for a minimization, the calculation stops due to bad
energies. Do you know how to solve this issue?


This isn't a pdb2gmx problem so much as it is a quirk of how CHARMM-GUI 
creates lipid membranes. There is almost always overlap between tail 
atoms in the different lipid leaflets. The CHARMM minimizer deals with 
these just fine, but GROMACS almost always chokes. The reason is that 
GROMACS sets a rather aggressive default EM step size of 0.02 nm, 
whereas the CHARMM minimizer defaults to 0.002. Lower the value of 
emstep and see if it proceeds correctly. That has always worked for us.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Fatal error in grompp

2017-11-27 Thread Justin Lemkul




On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:

Dear All,

I want to calculate the interaction energy between water and protein
backbone. However, in mdp file, when I am using

energygrps = SOL backbone

grompp is returning the following error.

Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
different energy groups

Can someone kindly point out my mistake?


You can't make the backbone a separate energy group. Look at what atoms 
1 and 2 are - likely it's the N-terminal N and one H atom, which have to 
be in the same group to do a group-based, pairwise energy decomposition. 
Whatever groups you establish have to contain full charge groups.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

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Re: [gmx-users] Pdb files generated on Lincs warning

2017-11-27 Thread Justin Lemkul




On 11/27/17 1:04 AM, atb files wrote:
 

 
 Dear Users,When there is a Lincs warning (sometimes because of exceeding warnangle etc) the gromacs generates pdb files. My questions is:What is purpose of generating pdb files? What information they give? Which information we need to look for to analyse those pdbs. ThanksYogi Sent using Zoho Mail
 


These are the coordinates before and after applying constraints for each 
domain of the system. They are not PBC-corrected so they can be really 
hard to interpret. mdrun prints which atoms are having issues, which is 
usually sufficient to begin diagnosing what is going on.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

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http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] pH dependent simulation

2017-11-27 Thread Justin Lemkul




On 11/27/17 1:02 AM, Tasneem Kausar wrote:

pKa of amino acid residue is a constant quantity. Depending on the pH you


That's not strictly true. Titratable amino acids can be found in unique 
microenvironments that cause shifts in canonical values. For instance, 
there are some catalytic lysines known in hydrophobic environments that 
have pKa values of ~4 instead of the canonical value of ~10.5.


-Justin


can protonate and deprotonate amino acid according to the pKa of particular
residue.


Virus-free.
www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Mon, Nov 27, 2017 at 9:39 AM,  wrote:


Hello Everyone

I am trying to simulate a protein at two pH (7.4 and 9.0) using
gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
positively charged residues.

However upon predicting the pKa values using H++ server, I am getting the
same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
should have different pKa values at pH 7 and 9).

Whether I am in the right direction or doing something wrong!!!

Can anyone kindly suggest me how to proceed further?

Any suggestion is appreciated.

Thank You
Zaved


* * * D I S C L A I M E R * * *
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==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] pH dependent simulation

2017-11-27 Thread Justin Lemkul




On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote:

Hello Everyone

I am trying to simulate a protein at two pH (7.4 and 9.0) using
gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
positively charged residues.

However upon predicting the pKa values using H++ server, I am getting the
same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
should have different pKa values at pH 7 and 9).


Why do you expect that? There are no amino acids with pKa in that range, 
so nothing should change unless there are unique microenvironments that 
shift canonical pKa values. As H++ has not detected any, likely your 
protein behaves canonically. You can confirm your calculated pKa values 
with another method, like PROPKA, to be sure.


-Justin


Whether I am in the right direction or doing something wrong!!!

Can anyone kindly suggest me how to proceed further?

Any suggestion is appreciated.

Thank You
Zaved


* * * D I S C L A I M E R * * *
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free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.


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==

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Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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[gmx-users] Not enough memory. Failed to realloc

2017-11-27 Thread RAHUL SURESH

Dear Users

I am trying to carryout protein-metal interaction using charmm36 ff. During
solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro"
*i receive a error stating








*"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
atoms_->atom,atoms_->atom=0(called from
file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line
86)". *
I have enough space to carry out this simulation and I am using 2016
version of gromacs.

I couldnt diagonise the error exactly. Any help on this will be of great
use.

Thank you

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] Pdb2gmx melts molecules due to bad distances

2017-11-27 Thread GIANMARCO BARTALINI

Hello guys, I produced a system "protein + lipid membrane" using the online
tool CHARMM-GUI. Since I need to use the Amber force field, I added the
Lipids17 force field inside Gromacs. The implementation should work fine,
since the conversion of an equilibrated structure produces a nice and
correct gro file. But when I try to convert the (not minimized) PDB file
that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
lipid molecules are melted together (due to their bad distances). If I use
this structure for a minimization, the calculation stops due to bad
energies. Do you know how to solve this issue?
Thank you in advance,

Gianmarco
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Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

2017-11-27 Thread CHAN, Zoe ZC [Student]

Dear Gerrit,

Thank you very much for your prompt reply.
I’ve tried to run the simulation with wenjin’s tutorial and it passed the point 
charge correction step with no problem. I compared the “.out” output files of 
my protein and of the tutorial peptide, I noticed there’s a line “%pointcharges 
“peptide.pc”” at the end of the input file section, I guess it shows that the 
basename has been linked to the “.pc” point charge file instead of the default 
name “temp.pc”, and it’s missing in my protein’s output file. Would that have 
possibly caused the crash?
Again, thank you for your help.

Best regards,
Zoe

On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit 
mailto:ggro...@gwdg.de>> wrote:

From the error message it seems that ORCA program crashes. Unfortunately, Orca 
is no longer supported, which means that if the ORCA's input or anything else 
has changed, the gromacs interface may fail.

What you could try is to use the version of ORCA that others have used before.

Best,

Gerrit





Content-Type: text/plain; charset="iso-8859-1"

Dear Gromacs Users,


I've been running a QM/MM calculation on a protein with fluorescence probe, 
using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1.  The following 
lines were included in the .mdp file,


QMMM = yes
QMMM-grps= QMatoms
QMmethod  = B3LYP
QMbasis  = 6-31G*
QMMMscheme   = ONIOM
QMcharge   = -2
QMmult= 2

The run was aborted with the error messages,


FATAL ERROR ENCOUNTERED
CANNOT OPEN FILE
Filename: temp.pc

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee]
[ 2] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98]
[ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0]
[ 4] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647]
[ 5] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9]
[ 6] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b]
[ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef]
[ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33]
[ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172]
[10] mdrun_mpi_d(cmain+0x1a17)[0x433f67]
[11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830]
[12] mdrun_mpi_d(_start+0x29)[0x4072b9]
*** End of error message ***
Segmentation fault (core dumped)


I am clueless on where the error came from, would anyone have any insight?  
Thank you.


Best regards,

Zoe

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www.polyu.edu.hk/80anniversary

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[gmx-users] Fatal error in grompp

2017-11-27 Thread Saumyak Mukherjee

Dear All,

I want to calculate the interaction energy between water and protein
backbone. However, in mdp file, when I am using

energygrps = SOL backbone

grompp is returning the following error.

Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
different energy groups

Can someone kindly point out my mistake?

Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.‌
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Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

2017-11-27 Thread Groenhof, Gerrit

>From the error message it seems that ORCA program crashes. Unfortunately, Orca 
>is no longer supported, which means that if the ORCA's input or anything else 
>has changed, the gromacs interface may fail.

What you could try is to use the version of ORCA that others have used before.

Best,

Gerrit
 




Content-Type: text/plain; charset="iso-8859-1"

Dear Gromacs Users,


I've been running a QM/MM calculation on a protein with fluorescence probe, 
using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1.  The following 
lines were included in the .mdp file,


QMMM = yes
QMMM-grps= QMatoms
QMmethod  = B3LYP
QMbasis  = 6-31G*
QMMMscheme   = ONIOM
QMcharge   = -2
QMmult= 2

The run was aborted with the error messages,


FATAL ERROR ENCOUNTERED
CANNOT OPEN FILE
Filename: temp.pc

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee]
[ 2] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98]
[ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0]
[ 4] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647]
[ 5] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9]
[ 6] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b]
[ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef]
[ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33]
[ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172]
[10] mdrun_mpi_d(cmain+0x1a17)[0x433f67]
[11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830]
[12] mdrun_mpi_d(_start+0x29)[0x4072b9]
*** End of error message ***
Segmentation fault (core dumped)


I am clueless on where the error came from, would anyone have any insight?  
Thank you.


Best regards,

Zoe

[http://mlm.polyu.edu.hk/PolyU80_Email_Signature.png]

www.polyu.edu.hk/80anniversary

Disclaimer:

This message (including any attachments) contains confidential information 
intended for a specific individual and purpose. If you are not the intended 
recipient, you should delete this message and notify the sender and The Hong 
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copying, or distribution of this message, or the taking of any action based on 
it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or 
quality of information obtained through University E-mail Facilities. Any views 
and opinions expressed are only those of the author(s) and do not necessarily 
represent those of the University and the University accepts no liability 
whatsoever for any losses or damages incurred or caused to any party as a 
result of the use of such information.


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Re: [gmx-users] Simulation on multi nodes performance

2017-11-27 Thread Mark Abraham

Hi,

There's some useful background at
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html

Whether you want mpirun -np X mdrun_mpi or mpirun -np X gmx_mpi mdrun
depends whether GROMACS was configured to build only mdrun.

Otherwise, the logfile is indeed your friend - so that you can see whether
mdrun agreed with what you thought the hardware was, and in the performance
report at the end to see what took lots of time.

Mark

On Mon, Nov 27, 2017 at 7:21 AM Ali Ahmed  wrote:

> Hello GMX users
>
> I'm trying to do simulations on multi nodes so I used  8 nodes (128
> processors). AS I see there is no difference between 1 node and 8 nodes.
>
> I used these commands:
>
> ---
>
> load apps/gromacs-2016
>
> load apps/openmpi-2.1.1
>
> gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr
>
> mpirun -np 128 mdrun_mpi -v -deffnm EMZ
>
> 
>
> I'm kind of confused about the right commands
>
> Any comment will be helpful
>
> Thanks in advance
>
> Ali
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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Re: [gmx-users] Simulation on multi nodes performance

2017-11-27 Thread Alexandr Nasedkin


On 27/11/2017 07:21, Ali Ahmed wrote:Hello GMX users

I'm trying to do simulations on multi nodes so I used  8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.
Check the log file showing how many nodes you use, look for a line as in 
template:

Running on 2 nodes with total 40 cores, 40 logical cores


I used these commands:

---

load apps/gromacs-2016

load apps/openmpi-2.1.1

gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr

mpirun -np 128 mdrun_mpi -v -deffnm EMZ



I'm kind of confused about the right commands
I use gmx mdrun_mpi instead of mdrun_mpi: all depends on how your 
gromacs is installed.


Any comment will be helpful

Thanks in advance

Ali

-Alex

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[gmx-users] QM/MM-ORCA Point Charge Correction Error

2017-11-27 Thread Zoe Chan

Dear Gromacs Users,


I've been running a QM/MM calculation on a protein with fluorescence probe, 
using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1.  The following 
lines were included in the .mdp file,


QMMM = yes
QMMM-grps= QMatoms
QMmethod  = B3LYP
QMbasis  = 6-31G*
QMMMscheme   = ONIOM
QMcharge   = -2
QMmult= 2

The run was aborted with the error messages,


FATAL ERROR ENCOUNTERED
CANNOT OPEN FILE
Filename: temp.pc

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee]
[ 2] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98]
[ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0]
[ 4] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647]
[ 5] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9]
[ 6] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b]
[ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef]
[ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33]
[ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172]
[10] mdrun_mpi_d(cmain+0x1a17)[0x433f67]
[11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830]
[12] mdrun_mpi_d(_start+0x29)[0x4072b9]
*** End of error message ***
Segmentation fault (core dumped)


I am clueless on where the error came from, would anyone have any insight?  
Thank you.


Best regards,

Zoe

[http://mlm.polyu.edu.hk/PolyU80_Email_Signature.png]

www.polyu.edu.hk/80anniversary

Disclaimer:

This message (including any attachments) contains confidential information 
intended for a specific individual and purpose. If you are not the intended 
recipient, you should delete this message and notify the sender and The Hong 
Kong Polytechnic University (the University) immediately. Any disclosure, 
copying, or distribution of this message, or the taking of any action based on 
it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or 
quality of information obtained through University E-mail Facilities. Any views 
and opinions expressed are only those of the author(s) and do not necessarily 
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whatsoever for any losses or damages incurred or caused to any party as a 
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[gmx-users] Pdb files generated on Lincs warning

2017-11-27 Thread atb files





Dear Users,When there is a Lincs warning (sometimes because of 
exceeding warnangle etc) the gromacs generates pdb files. My questions is:What 
is purpose of generating pdb files? What information they give? Which 
information we need to look for to analyse those pdbs. ThanksYogi Sent using 
Zoho Mail  






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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

Re: [gmx-users] Umbrella sampling

Re: [gmx-users] Not enough memory. Failed to realloc

Re: [gmx-users] Not enough memory. Failed to realloc

Re: [gmx-users] Not enough memory. Failed to realloc

Re: [gmx-users] Fatal error in grompp

Re: [gmx-users] Fatal error in grompp

Re: [gmx-users] Build thin film.

Re: [gmx-users] Not enough memory. Failed to realloc

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Re: [gmx-users] Performance test

Re: [gmx-users] Not enough memory. Failed to realloc

Re: [gmx-users] pH dependent simulation

[gmx-users] SPC/Fw model of water

Re: [gmx-users] Not enough memory. Failed to realloc

Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

Re: [gmx-users] Fatal error in grompp

Re: [gmx-users] Pdb files generated on Lincs warning

Re: [gmx-users] pH dependent simulation

Re: [gmx-users] pH dependent simulation

[gmx-users] Not enough memory. Failed to realloc

[gmx-users] Pdb2gmx melts molecules due to bad distances

Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

[gmx-users] Fatal error in grompp

Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Re: [gmx-users] Simulation on multi nodes performance

Re: [gmx-users] Simulation on multi nodes performance

[gmx-users] QM/MM-ORCA Point Charge Correction Error

[gmx-users] Pdb files generated on Lincs warning

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