date:20150311

[gmx-users] Binding free energy of an ion from alchemical transformation

2015-03-11 Thread Wojciech Kopeć

Dear Gromacs users,

I'm thinking about performing free energy calculations for a protein that
binds cations,  using alchemical transformation method. In the simplest
case I'd transform an ion (one atom) into a naked particle; however in this
case I'd get a non-zero overall charge of the system during the charge
decoupling. I'm aware of some corrections for that and also that Gromacs
probably neutralises the charge with PME (?). Another approach I've been
thinking of is to simultaneously couple a naked particle somewhere in the
bulk with the environment, switching on the charge in a same way as the
charge of the ion is being switched off. In this way, the charge would be 0
all the time, and at the end of the simulation would yield the protein with
an empty binding site and the ion somewhere in the bulk. Are there any
obvious pitfalls with this approach?

Thank you,
Wojciech
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[gmx-users] umbrella sampling tutorial

2015-03-11 Thread Ming Tang

Dear all,

I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous pulling 
simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code, but 
failed.

; Pull code in tutorial
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2

; COM pulling I modified
pull= umbrella
pull_geometry= distance  ; simple distance increase
pull_dim = N N Y
pull_start   = yes   ; define initial COM distance > 0
pull_coord1-groups   = 2
pull-group1-name = Chain_B
pull_group2-name = Chain_A
pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k= 1000  ; kJ mol^-1 nm^-2

Fatal error:
Group Chain_B referenced in the .mdp file was not found in the 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.

Index:
[ r_1-27 ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
 106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
 121  122  123  124  125  126  127  128  129  130  131  132  133  134  135
 136  137  138  139  140  141  142  143  144  145  146  147  148  149  150
 151  152  153  154  155  156  157  158  159  160  161  162  163  164  165
 166  167  168  169  170  171  172  173  174  175  176  177  178  179  180
 181  182  183  184  185  186  187  188  189  190  191  192  193  194  195
 196  197  198  199  200  201  202  203  204  205  206  207  208  209  210
 211  212  213  214  215  216  217  218  219  220  221  222  223  224  225
 226
[ r_28-54 ]
227  228  229  230  231  232  233  234  235  236  237  238  239  240  241
 242  243  244  245  246  247  248  249  250  251  252  253  254  255  256
 257  258  259  260  261  262  263  264  265  266  267  268  269  270  271
 272  273  274  275  276  277  278  279  280  281  282  283  284  285  286
 287  288  289  290  291  292  293  294  295  296  297  298  299  300  301
 302  303  304  305  306  307  308  309  310  311  312  313  314  315  316
 317  318  319  320  321  322  323  324  325  326  327  328  329  330  331
 332  333  334  335  336  337  338  339  340  341  342  343  344  345  346
 347  348  349  350  351  352  353  354  355  356  357  358  359  360  361
 362  363  364  365  366  367  368  369  370  371  372  373  374  375  376
 377  378  379  380  381  382  383  384  385  386  387  388  389  390  391
 392  393  394  395  396  397  398  399  400  401  402  403  404  405  406
 407  408  409  410  411  412  413  414  415  416  417  418  419  420  421
 422  423  424  425  426  427  428  429  430  431  432  433  434  435  436
 437  438  439  440  441  442  443  444  445  446  447  448  449  450  451
 452

Could anybody tell me what's wrong with the COM pulling code I modified?

Thanks in advance!

Regards,

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Re: [gmx-users] enemat output

2015-03-11 Thread Mark Abraham

On 11/03/2015 3:44 am, "Diogo Martins de Sá"  wrote:
>
> Hi guys,
>
> Can any one show a picture of how a normal enemat output should look
> like?
>
> Since the bug in enemat was only fixed in version 4.6.5, I have a very
> basic question:
>
> Can I install a newer version of gromac (say 5) and use its enemat to
> treat .edr files from older versions (i.e. 4.5.3 and 4.6.3)??

Yes

Mark

> Many thanks
>
> Diogo
>
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[gmx-users] g_anaeig error

2015-03-11 Thread tasneem kausar

for PCA i used the g_covar followed by g_anaeig.
for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
these files are generated by g_covar.
g_anaeig gives the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?
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[gmx-users] Thermostats and MSD

2015-03-11 Thread sujithkakkat .

Dear all,

  I am simulating a system of small hydrophobic solutes ( CH4)  dissolved
in water. Simulations are performed in the NPT simulation, and I would like
to determine the diffusion coefficients from MSD plots. I have two related
questions;

(1)  Is the thermostat going to seriously affect the diffusivity of the
molecules. I am using Nose-Hoover thermostat with a time constant of 0.2
ps. Is the choice of time constant very crucial while studying diffusivity.
Should I avoid thermostat and go for NVE simulations for studying
diffusivity.

(2) From radial distribution functions, it is found that there is
association between the hydrophobic solvents. I would like to know, if in
case a small cluster of the hydrophobic solutes are formed, then the
whether the rotational motion of these clusters contribute to dispalcement
in the MSD calculation.

Please comment.

Regards,
Sujith.
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Re: [gmx-users] g_anaeig error

2015-03-11 Thread Tsjerk Wassenaar

Hi Tasneem,

Please provide a complete workflow, with commands and selections.

Cheers,

Tsjerk

On Wed, Mar 11, 2015 at 10:31 AM, tasneem kausar 
wrote:

> for PCA i used the g_covar followed by g_anaeig.
> for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
> these files are generated by g_covar.
> g_anaeig gives the following message;
> There were 40 inconsistent shifts. Check your topology
> where is the problem occured?
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Compiler

2015-03-11 Thread melichercik

Hello Alex,
this is problem of CUDA library, not Gromacs itself. I'm not sure, if using the 
newest CUDA 6.5.19 solved for me this problem or I needed to compile with 
Intel-14. But deffinitelly your complain should go to nVidia, not Gromacs team.

Milan

On Wed, Mar 11, 2015 at 09:49:50AM +, Alexander Tzanov wrote:
> Dear all I am trying to install the 5.0.4 with GPU support with Intel 15 
> compiler and 1.8.4 openmpi.I got errors that  only Intel 14 is supported. Is 
> this true? And if so do you plan to have tested/port GMX with latest Intel 
> compiler?
> 
> Thanks Alex
> 
> 
> Connect with CSI on Social Media>
> -- 
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[gmx-users] add. residue in topology database

2015-03-11 Thread Daniele Veclani

Dear users

I'm trying to build the topology files for a box with 1000 molecules of
water and an organic molecule.

when I use pdb2gmx come out the error: "OUB7 not found in residue topology
database"

how do I put this residue in the database?

I have a .itp file for this molecule.

I use gromacs 5.0.4.

Best regards.
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 49

2015-03-11 Thread tasneem kausar

for PCA i used the g_covar followed by g_anaeig.
i used the command line for g_covr as
g_covar -f full.xtc -s full.tpr -o eig.xvg
I have selected the protein for least square fit and main chain for
covarience analysis.
There is a warning message.
WARNING: number of atoms in tpx (312) and trajectory (1061) do not match

The abve comman gave the files average.pdb, eigenvec.trr and eig.xvg
Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
The commnan line for g_anaeig is given below.
g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
For least square fit i have selected the protein and same for the
eigenvectors
This gave the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?

On Wed, Mar 11, 2015 at 3:31 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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>
>
> Today's Topics:
>
>1. Binding free energy of an ion from alchemical transformation
>   (Wojciech Kope?)
>2. umbrella sampling tutorial (Ming Tang)
>3. Re: enemat output (Mark Abraham)
>4. g_anaeig error (tasneem kausar)
>5. Thermostats and MSD (sujithkakkat .)
>6. Re: g_anaeig error (Tsjerk Wassenaar)
>7. Compiler (Alexander Tzanov)
>
>
> --
>
> Message: 1
> Date: Wed, 11 Mar 2015 09:23:53 +0100
> From: Wojciech Kope? <9000...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Binding free energy of an ion from alchemical
> transformation
> Message-ID:
> <
> cak_bonfb_m2mgxumw8gswhfzbtdifp4lkjw4pgbhvy3p5uc...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I'm thinking about performing free energy calculations for a protein that
> binds cations,  using alchemical transformation method. In the simplest
> case I'd transform an ion (one atom) into a naked particle; however in this
> case I'd get a non-zero overall charge of the system during the charge
> decoupling. I'm aware of some corrections for that and also that Gromacs
> probably neutralises the charge with PME (?). Another approach I've been
> thinking of is to simultaneously couple a naked particle somewhere in the
> bulk with the environment, switching on the charge in a same way as the
> charge of the ion is being switched off. In this way, the charge would be 0
> all the time, and at the end of the simulation would yield the protein with
> an empty binding site and the ion somewhere in the bulk. Are there any
> obvious pitfalls with this approach?
>
> Thank you,
> Wojciech
>
>
> --
>
> Message: 2
> Date: Wed, 11 Mar 2015 08:17:42 +
> From: Ming Tang 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: [gmx-users] umbrella sampling tutorial
> Message-ID:
> <
> dm2pr0101mb10690504f9ed567db577b697b6...@dm2pr0101mb1069.prod.exchangelabs.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> I was learning the Umbrella Sampling tutorial step by step on Gromacs
> 5.0.4.
> Everything was fine until I got to the step five (run the continuous
> pulling simulation).
> Then I turned to the 5.0.4 manual, and tried to modify the pull code, but
> failed.
>
> ; Pull code in tutorial
> pull= umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim= N N Y
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = Chain_B
> pull_group1 = Chain_A
> pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
> ; COM pulling I modified
> pull= umbrella
> pull_geometry= distance  ; simple distance increase
> pull_dim = N N Y
> pull_start   = yes   ; define initial COM distance > 0
> pull_coord1-groups   = 2
> pull-group1-name = Chain_B
> pull_group2-name = Chain_A
> pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k= 1000  ; kJ mol^-1 nm^-2
>
> Fatal error:
> Group Chain_B referenced in the .mdp file was not found in the 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.
>
> Index:
> [ r_1-27 ]
>12345

Re: [gmx-users] Compiler

2015-03-11 Thread Mark Abraham

Hi,

Indeed, this is a CUDA property - only certain compiler versions are
supported with certain CUDA versions. People have been known to hack out
the check and things work fine, but obviously you're own your own there...
You should also compare performance with gcc, which is sometimes better.

Mark

On Wed, Mar 11, 2015 at 11:14 AM,  wrote:

> Hello Alex,
> this is problem of CUDA library, not Gromacs itself. I'm not sure, if
> using the newest CUDA 6.5.19 solved for me this problem or I needed to
> compile with Intel-14. But deffinitelly your complain should go to nVidia,
> not Gromacs team.
>
> Milan
>
> On Wed, Mar 11, 2015 at 09:49:50AM +, Alexander Tzanov wrote:
> > Dear all I am trying to install the 5.0.4 with GPU support with Intel 15
> compiler and 1.8.4 openmpi.I got errors that  only Intel 14 is supported.
> Is this true? And if so do you plan to have tested/port GMX with latest
> Intel compiler?
> >
> > Thanks Alex
> >
> > 
> > Connect with CSI on Social Media>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
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> >
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Compiler

2015-03-11 Thread Alexander Tzanov

Thanks a lot  Milan.I will try nVidia channel. Thanks a lot.
Alex

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 
melicher...@leaf.nh.cas.cz [melicher...@leaf.nh.cas.cz]
Sent: Wednesday, March 11, 2015 6:14 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Compiler

Hello Alex,
this is problem of CUDA library, not Gromacs itself. I'm not sure, if using the 
newest CUDA 6.5.19 solved for me this problem or I needed to compile with 
Intel-14. But deffinitelly your complain should go to nVidia, not Gromacs team.

Milan

On Wed, Mar 11, 2015 at 09:49:50AM +, Alexander Tzanov wrote:
> Dear all I am trying to install the 5.0.4 with GPU support with Intel 15 
> compiler and 1.8.4 openmpi.I got errors that  only Intel 14 is supported. Is 
> this true? And if so do you plan to have tested/port GMX with latest Intel 
> compiler?
>
> Thanks Alex
>
> 
> Connect with CSI on Social Media>
> --
> Gromacs Users mailing list
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> * Please search the archive at 
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Connect with CSI on Social Media>
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Re: [gmx-users] Thermostats and MSD

2015-03-11 Thread Michael Shirts

For #1, see: http://pubs.acs.org/doi/abs/10.1021/ct400109a

For #2, I think you'll have to figure that out for yourself.

On Wed, Mar 11, 2015 at 5:42 AM, sujithkakkat . 
wrote:

> Dear all,
>
>   I am simulating a system of small hydrophobic solutes ( CH4)  dissolved
> in water. Simulations are performed in the NPT simulation, and I would like
> to determine the diffusion coefficients from MSD plots. I have two related
> questions;
>
> (1)  Is the thermostat going to seriously affect the diffusivity of the
> molecules. I am using Nose-Hoover thermostat with a time constant of 0.2
> ps. Is the choice of time constant very crucial while studying diffusivity.
> Should I avoid thermostat and go for NVE simulations for studying
> diffusivity.
>
> (2) From radial distribution functions, it is found that there is
> association between the hydrophobic solvents. I would like to know, if in
> case a small cluster of the hydrophobic solutes are formed, then the
> whether the rotational motion of these clusters contribute to dispalcement
> in the MSD calculation.
>
> Please comment.
>
> Regards,
> Sujith.
> --
> Gromacs Users mailing list
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Re: [gmx-users] umbrella sampling tutorial

2015-03-11 Thread Justin Lemkul




On 3/11/15 4:17 AM, Ming Tang wrote:

Dear all,

I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous pulling 
simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code, but 
failed.

; Pull code in tutorial
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2

; COM pulling I modified
pull= umbrella
pull_geometry= distance  ; simple distance increase
pull_dim = N N Y
pull_start   = yes   ; define initial COM distance > 0
pull_coord1-groups   = 2
pull-group1-name = Chain_B
pull_group2-name = Chain_A
pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k= 1000  ; kJ mol^-1 nm^-2

Fatal error:
Group Chain_B referenced in the .mdp file was not found in the 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.

Index:
[ r_1-27 ]
123456789   10   11   12   13   14   15
   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
   91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135
  136  137  138  139  140  141  142  143  144  145  146  147  148  149  150
  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165
  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180
  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195
  196  197  198  199  200  201  202  203  204  205  206  207  208  209  210
  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225
  226
[ r_28-54 ]
227  228  229  230  231  232  233  234  235  236  237  238  239  240  241
  242  243  244  245  246  247  248  249  250  251  252  253  254  255  256
  257  258  259  260  261  262  263  264  265  266  267  268  269  270  271
  272  273  274  275  276  277  278  279  280  281  282  283  284  285  286
  287  288  289  290  291  292  293  294  295  296  297  298  299  300  301
  302  303  304  305  306  307  308  309  310  311  312  313  314  315  316
  317  318  319  320  321  322  323  324  325  326  327  328  329  330  331
  332  333  334  335  336  337  338  339  340  341  342  343  344  345  346
  347  348  349  350  351  352  353  354  355  356  357  358  359  360  361
  362  363  364  365  366  367  368  369  370  371  372  373  374  375  376
  377  378  379  380  381  382  383  384  385  386  387  388  389  390  391
  392  393  394  395  396  397  398  399  400  401  402  403  404  405  406
  407  408  409  410  411  412  413  414  415  416  417  418  419  420  421
  422  423  424  425  426  427  428  429  430  431  432  433  434  435  436
  437  438  439  440  441  442  443  444  445  446  447  448  449  450  451
  452

Could anybody tell me what's wrong with the COM pulling code I modified?



The groups have not been named Chain_A and Chain_B, but that's how you're 
attempting to use them.  Rename them in the .ndx or .mdp.


-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] add. residue in topology database

2015-03-11 Thread Justin Lemkul




On 3/11/15 6:22 AM, Daniele Veclani wrote:

Dear users

I'm trying to build the topology files for a box with 1000 molecules of
water and an organic molecule.

when I use pdb2gmx come out the error: "OUB7 not found in residue topology
database"

how do I put this residue in the database?

I have a .itp file for this molecule.



If you have an .itp file, you don't need pdb2gmx at all.  The topology for an 
organic molecule in water is trivially simple:


#include (parent force field)
#include water_model.itp
#include organic_molecule.itp

[ system ]
whatever

[ molecules ]
organic 1
water   N

If you want to add it to the .rtp, see 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
but you'll just be investing a lot of unnecessary time when the above approach 
takes a few moments in a text editor.


-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] add. residue in topology database

2015-03-11 Thread Daniele Veclani

Thank you Justin.

2015-03-11 12:33 GMT+01:00 Justin Lemkul :

>
>
> On 3/11/15 6:22 AM, Daniele Veclani wrote:
>
>> Dear users
>>
>> I'm trying to build the topology files for a box with 1000 molecules of
>> water and an organic molecule.
>>
>> when I use pdb2gmx come out the error: "OUB7 not found in residue topology
>> database"
>>
>> how do I put this residue in the database?
>>
>> I have a .itp file for this molecule.
>>
>>
> If you have an .itp file, you don't need pdb2gmx at all.  The topology for
> an organic molecule in water is trivially simple:
>
> #include (parent force field)
> #include water_model.itp
> #include organic_molecule.itp
>
> [ system ]
> whatever
>
> [ molecules ]
> organic 1
> water   N
>
> If you want to add it to the .rtp, see http://www.gromacs.org/
> Documentation/How-tos/Adding_a_Residue_to_a_Force_Field but you'll just
> be investing a lot of unnecessary time when the above approach takes a few
> moments in a text editor.
>
> -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] Comparing two Ptn-Ptn docking models

2015-03-11 Thread Justin Lemkul




On 3/10/15 11:59 PM, Diogo Martins de Sá wrote:

Thanks for the advice Justin!

I'm looking in to it right now.

My box has the following dimensions:
9.10300  12.10200  11.46200

How would you define "continuous pull", is it pull in which the distance
increases indefinitely but slow enough not to trespass the distance
limits/conditions? I get the part where the periodic images can't


There's no real "limit," per se, but you need to decide on a suitably long 
reaction coordinate to achieve separation of the proteins.



interact and the "less than one half the length of the box" condition.
But how do I know if my box and my system are apt for umbrella sampling?


Decide on the length of the reaction coordinate that will be sufficient to 
separate your proteins, translate one subunit out that far (editconf or trjconv) 
and build a box around it of suitable size.  That's the size you need for every 
window (the system doesn't change between windows).



will I be able to use mdrun -rerun with my current system?



No, umbrella sampling is a totally new set of simulations.

-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] g_rotacf and P 1,2,3 meaning

2015-03-11 Thread Jennifer Vo

Dear All,
When using g_rotacf, could you please explain to me the difference between
option P 1, 2, and 3? The results from these are significantly different.
Many thanks in advance.
Regards,
Jennifer
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[gmx-users] fine-grained and coarse-grained

2015-03-11 Thread Rebeca García Fandiño

Dear Gromacs users,
a general question...would it have any sense to mixture into a single 
simulation coarse-grained and fine-grained parameters?
Thanks a lot for your help,
Best wishes,

Rebeca

Dr. Rebeca Garcia
Santiago de Compostela University
Spain

  
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[gmx-users] Cardiolipin in insane.py (MARTINI)

2015-03-11 Thread shivangi nangia

Hello,

I want to make a bilayer of POPC and cardiolipin.

Since Cardiolipin is not included in insane.py, could you please provide
some options/suggestions to generate the bi-layer.


Self-assembly is a little tricky to handle.


Thanks,
sxn
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Re: [gmx-users] Cardiolipin in insane.py (MARTINI)

2015-03-11 Thread Tsjerk Wassenaar

Hi sxn,

In fact, cardiolipin is available in insane. I should probably check the
version on the site... In addition, it is quite trivial to add (more)
cardiolipin(s). I'll send you the latest version shortly...

Cheers,

Tsjerk
On Mar 11, 2015 5:14 PM, "shivangi nangia" 
wrote:

> Hello,
>
> I want to make a bilayer of POPC and cardiolipin.
>
> Since Cardiolipin is not included in insane.py, could you please provide
> some options/suggestions to generate the bi-layer.
>
>
> Self-assembly is a little tricky to handle.
>
>
> Thanks,
> sxn
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Re: [gmx-users] Cardiolipin in insane.py (MARTINI)

2015-03-11 Thread shivangi nangia

Thanks so much Tsjerk.

I looked for the latest version on the MARTINI page (
http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/239-insane) but
could not find Cardiolipin in it.


Thanks so much for the help.




sxn

On Wed, Mar 11, 2015 at 12:54 PM, Tsjerk Wassenaar 
wrote:

> Hi sxn,
>
> In fact, cardiolipin is available in insane. I should probably check the
> version on the site... In addition, it is quite trivial to add (more)
> cardiolipin(s). I'll send you the latest version shortly...
>
> Cheers,
>
> Tsjerk
> On Mar 11, 2015 5:14 PM, "shivangi nangia" 
> wrote:
>
> > Hello,
> >
> > I want to make a bilayer of POPC and cardiolipin.
> >
> > Since Cardiolipin is not included in insane.py, could you please provide
> > some options/suggestions to generate the bi-layer.
> >
> >
> > Self-assembly is a little tricky to handle.
> >
> >
> > Thanks,
> > sxn
> > --
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[gmx-users] Query- Advice needed

2015-03-11 Thread Priya Das

Dear all,

I am working with a membrane bound ion channel. If a ligand binds in the
pore lumen, it occludes the pore and prevent entry of ions.
I have got docking results showing that the ligand binds ion channel.For an
intensive explanation regarding binding of the ligand, i need to prove it
by dynamics studies.
My query is that:

1) Should i simulate the ion channel in DPPC/ POPC membrane so as to get
different conformations of the ion channel (open to closed) and then dock
different models with the ligand?

2) Should i simulate ligand bound ion channel in DPPC/ POPC membrane to
check the stability?

3) Should i use steered dynamics along with conventional molecular dynamics
to show different possible conformations of the ligand along the ion
channel?



-- 
*Let us all join hands to save our " Mother Earth"*

Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala
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[gmx-users] Segmentation fault

2015-03-11 Thread Wim Rm Cardoen

Hello,

I have compiled the latest version of gromacs (5.0.4) on our cluster (RHEL6 OS)
using the intel compiler (2015.1.133) as well as mvapich2 2.0 compiled with the 
same version of the INTEL compiler.
For the FFTW and the BLAS/LAPACK I used Intel MKL's library.
When I tested the regression test ALL tests failed due to segmentation faults 
at the MPI level.
Help would be strongly appreciated.

Thanks ,

Wim

I compiled gromacs 5.0.4 with the following flags (Non-threaded and non-gpu 
version)

cmake .. 
-DCMAKE_INSTALL_PREFIX=/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i
 \
 -DCMAKE_C_COMPILER=/uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpicc \
 
-DCMAKE_CXX_COMPILER=/uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpicxx \
 -DCMAKE_INCLUDE_PATH=" 
-I/uufs/ember.arches/sys/pkg/mvapich2/2.0i/include  
-I/uufs/chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/mkl/include/fftw " \
 -DCMAKE_LIBRARY_PATH=" 
-Wl,-rpath=/uufs/ember.arches/sys/pkg/mvapich2/2.0i/lib  
-L/uufs/ember.arches/sys/pkg/mvapich2/2.0i/lib -lmpich  
-Wl,-rpath=/uufs/chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/mkl/lib/intel64
  -L/uufs/chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/mkl/lib/intel64 
-lmkl_core -lmkl_intel_lp64 -lmkl_sequential  
-Wl,-rpath=/uufs/chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/lib/intel64  
-L/uufs/chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/lib/intel64 -limf 
-lifcore " \
  -DGMX_MPI=on  -DGMX_DOUBLE=ON  -DGMX_FFT_LIBRARY=mkl  
-DGMX_BUILD_MANUAL=on \
  -DGMX_OPENMP=OFF  -DGMX_THREAD_MPI=OFF
make -j 6
make check
# 100% tests passed, 0 tests failed out of 15
#
# Label Time Summary:
# GTest  =   5.77 sec
# IntegrationTest=  24.73 sec
# UnitTest   =   5.77 sec

make install


# Regression tests
wget http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz
tar -zxvf 
regressiontests-5.0.4.tar.gz
cd regressiontests-5.0.4
module load intel/2015.1.133
module load mvapich2/2.0.em.i
source 
/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/GMXRC
which mdrun_mpi_d
# 
/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/mdrun_mpi_d
which mpirun
# /uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpirun
./gmxtest.pl -np 12 -verbose -double  -mdrun  
/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/mdrun_mpi_d
   -mpirun /uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpirun simple


# 
-
Abnormal return value for '/uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpirun 
-np 12 -wdir 
/uufs/chpc.utah.edu/common/home/u0253283/regressiontests-5.0.4/simple/rb125 
/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/mdrun_mpi_d
  -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in rb125 for rb125
16 out of 16 simple tests FAILED

GROMACS:  gmx mdrun, VERSION 5.0.4 (double precision)
Executable:   
/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/gmx_mpi_d
Library dir:  
/uufs/chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/share/gromacs/top
Command line:
  mdrun_mpi_d -notunepme

Reading file topol.tpr, VERSION 5.0.4 (double precision)
[em110:mpi_rank_0][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_1][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_3][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_4][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_9][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_2][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_5][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_6][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_7][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_8][error_sighandler] Caught error: Segmentation fault (signal 
11)
[em110:mpi_rank_11][error_sighandler] Caught error: Segmentation fault (signal 
11)


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Re: [gmx-users] umbrella sampling tutorial

2015-03-11 Thread Ming Tang

Dear Justin,

Thanks for your help.
I changed the group names to Chain_A and Chain_B in my index file, and modified 
the COM pulling code.

; COM pulling
pull= umbrella
pull_geometry   = distance  ; simple distance increase 
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull-ngroups= 1
?assign the reference group?
pull-group1-name= Chain_A
pull-coord1-rate  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k = 1000  ; kJ mol^-1 nm^-2

But I didn't found the order to assign the reference group Chain_B in GROMACS 
5.0.4
Could you give me some help?

Thanks,
Ming

-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: Wednesday, 11 March 2015 9:34 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/11/15 4:17 AM, Ming Tang wrote:
> Dear all,
>
> I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
> Everything was fine until I got to the step five (run the continuous pulling 
> simulation).
> Then I turned to the 5.0.4 manual, and tried to modify the pull code, but 
> failed.
>
> ; Pull code in tutorial
> pull= umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim= N N Y
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = Chain_B
> pull_group1 = Chain_A
> pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
> ; COM pulling I modified
> pull= umbrella
> pull_geometry= distance  ; simple distance increase
> pull_dim = N N Y
> pull_start   = yes   ; define initial COM distance > 0
> pull_coord1-groups   = 2
> pull-group1-name = Chain_B
> pull_group2-name = Chain_A
> pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k= 1000  ; kJ mol^-1 nm^-2
>
> Fatal error:
> Group Chain_B referenced in the .mdp file was not found in the 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.
>
> Index:
> [ r_1-27 ]
> 123456789   10   11   12   13   14   15
>16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
>   106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
>   121  122  123  124  125  126  127  128  129  130  131  132  133  134  135
>   136  137  138  139  140  141  142  143  144  145  146  147  148  149  150
>   151  152  153  154  155  156  157  158  159  160  161  162  163  164  165
>   166  167  168  169  170  171  172  173  174  175  176  177  178  179  180
>   181  182  183  184  185  186  187  188  189  190  191  192  193  194  195
>   196  197  198  199  200  201  202  203  204  205  206  207  208  209  210
>   211  212  213  214  215  216  217  218  219  220  221  222  223  224  225
>   226
> [ r_28-54 ]
> 227  228  229  230  231  232  233  234  235  236  237  238  239  240  241
>   242  243  244  245  246  247  248  249  250  251  252  253  254  255  256
>   257  258  259  260  261  262  263  264  265  266  267  268  269  270  271
>   272  273  274  275  276  277  278  279  280  281  282  283  284  285  286
>   287  288  289  290  291  292  293  294  295  296  297  298  299  300  301
>   302  303  304  305  306  307  308  309  310  311  312  313  314  315  316
>   317  318  319  320  321  322  323  324  325  326  327  328  329  330  331
>   332  333  334  335  336  337  338  339  340  341  342  343  344  345  346
>   347  348  349  350  351  352  353  354  355  356  357  358  359  360  361
>   362  363  364  365  366  367  368  369  370  371  372  373  374  375  376
>   377  378  379  380  381  382  383  384  385  386  387  388  389  390  391
>   392  393  394  395  396  397  398  399  400  401  402  403  404  405  406
>   407  408  409  410  411  412  413  414  415  416  417  418  419  420  421
>   422  423  424  425  426  427  428  429  430  431  432  433  434  435  436
>   437  438  439  440  441  442  443  444  445  446  447  448  449  450  451
>   452
>
> Could anybody tell me what's wrong with the COM pulling code I modified?
>

The groups have not been named Chain_A and Chain_B, but that's how you're 
attempting to use them.  Rename them in the .ndx or .mdp.

-Justin

--
===

Re: [gmx-users] umbrella sampling tutorial

2015-03-11 Thread Justin Lemkul




On 3/11/15 8:58 PM, Ming Tang wrote:

Dear Justin,

Thanks for your help.
I changed the group names to Chain_A and Chain_B in my index file, and modified 
the COM pulling code.

; COM pulling
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull-ngroups= 1
?assign the reference group?
pull-group1-name= Chain_A
pull-coord1-rate  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k = 1000  ; kJ mol^-1 nm^-2

But I didn't found the order to assign the reference group Chain_B in GROMACS 
5.0.4
Could you give me some help?



Something like this (I haven't tested it, so please let me know if this 
works...or doesn't):


pull= umbrella
pull-geometry   = distance
pull-dim= N N Y
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= Chain_A
pull-group2-name= Chain_B
pull-coord1-rate= 0.01
pull-coord1-k   = 1000

-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] pdb2gmx and specbond with arbitrary ligand

2015-03-11 Thread Justin Lemkul




On 3/11/15 1:08 PM, Leandro Bortot wrote:

Dear users,

  I want to simulate some ligands covalently bonded to a protein, i.e.
covalent inhibitors. I've searched the list and found similar issues, but
mainly with heme in forcefields in which it is already supported. I use the
AMBER99SB-ILDN forcefield and I can simulate the non covalent complexes
with no problems using GAFF.

  I suppose I can just put both the ligand and the protein under the
same [moleculetype] specification in a .itp file and manually add the bonds
in this topology. It seems that I only need a script to renumber the atoms
to achieve this. However, I think pdb2gmx and specbond.dat may already be
able to do this. The problem is: How can pdb2gmx understand my arbitrary
ligand? Is adding my ligand to a local copy of
amber99sb-ildn/aminoacids.rtp the only way?

  What would be the best way to do that?



Yes, the .rtp approach is the most reliable way to do this.  Follow all the 
steps in 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
and add an entry in specbond.dat (format explained in 
http://www.gromacs.org/Documentation/File_Formats/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] umbrella sampling tutorial

2015-03-11 Thread Ming Tang

Hi Justin,

Your code works!
Thank you very much.

Regards,
Ming

-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: Thursday, 12 March 2015 11:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial

On 3/11/15 8:58 PM, Ming Tang wrote:
> Dear Justin,
>
> Thanks for your help.
> I changed the group names to Chain_A and Chain_B in my index file, and 
> modified the COM pulling code.
>
> ; COM pulling
> pull= umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim= N N Y
> pull_start  = yes   ; define initial COM distance > 0
> pull-ngroups= 1
> ?assign the reference group?
> pull-group1-name= Chain_A
> pull-coord1-rate  = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k = 1000  ; kJ mol^-1 nm^-2
>
> But I didn't found the order to assign the reference group Chain_B in 
> GROMACS 5.0.4 Could you give me some help?
>

Something like this (I haven't tested it, so please let me know if this 
works...or doesn't):

pull= umbrella
pull-geometry   = distance
pull-dim= N N Y
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= Chain_A
pull-group2-name= Chain_B
pull-coord1-rate= 0.01
pull-coord1-k   = 1000

-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] Dihedral angle autocorrelation function - g_chi function mismatch

2015-03-11 Thread atanu das

Hi All,
As Prof. David van der Spoel referred in the last communication about how the 
dihedral angle autocorrelation function is calculated via the program g_chi, I 
have a query regarding the differences that I found between the function 
mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function 
used by the program g_chi.
According to the article, the dihedral angle autocorrelation function is 
defined as:
C(t) =  . (Eq. 1 of the article)

However, the g_chi program uses the function:
C(t) =  . (Eq. 2)
So, apparently the g_chi program uses a different function. Am I correct? Is 
there a way around it? I mean is there a way to estimate C(t) using the 
function given in the article (Eq. 1)?
ThanksAtanu 
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[gmx-users] Force field choosing and parameterization

2015-03-11 Thread Gustavo Avelar Molina

Hi,

I'm new here and I barely have experience in GROMACS. I'm seeking some help
to solve an issue.

I want to run MD simulations of an enzyme that:

1 - Have a fluorescent probe attached next to the catalytic site;
2 - Have a polysaccharide (substrate) embedded in its catalytic site;

One simulation with both conditions at the same time, another with just the
first. I don't know yet if I'll need to use a QM/MM method. Maybe you could
help me to decide it too.

The objective is to correlate the MD simulations results to other
experimental results, such as fluorescence spectroscopy of the same system,
since the fluorophore emission spectrum changes in the presence of
substrate. By knowing the probe environment changes due to the substrate
presence in comparison to the system without it, one could explain the
experimental data, and vice versa. What I want to know is:

1 - Which force field would fit well on this system?
2 - Should I develop new parameters? If so, how can I properly do it?
3 - I've heard that I should develop new parameters considering the excited
state of the fluorophore. Is it really needed?

I think that's all for now.

Thanks.


==



Gustavo Avelar Molina, B.Sc. Chem.

M.Sc. Chem. Student



Departamento de Química

Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto

Laboratório de Bioquímica e Biofísica de Proteínas

Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil



+55 16 994311221 | +55 11 949874141

avelarmolinagust...@gmail.com | gustavoavelarmol...@usp.br

https://lbbpusp.wordpress.com/o-grupo/membros/gustavo/ |

https://www.researchgate.net/profile/Gustavo_Avelar_Molina

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[gmx-users] Force field choosing and parameterization

2015-03-11 Thread Gustavo Avelar Molina

Hi,

I'm new here and I barely have experience in GROMACS. I'm seeking some help
to solve an issue.

I want to run MD simulations of an enzyme that:

1 - Have a fluorescent probe attached next to the catalytic site;
2 - Have a polysaccharide (substrate) embedded in its catalytic site;

One simulation with both conditions at the same time, another with just the
first. I don't know yet if I'll need to use a QM/MM method. Maybe you could
help me to decide it too.

The objective is to correlate the MD simulations results to other
experimental results, such as fluorescence spectroscopy of the same system,
since the fluorophore emission spectrum changes in the substrate presence.
By knowing the probe environment changes due to the substrate presence in
comparison to the system without it, one could explain the experimental
data, and vice versa. What I want to know is:

1 - Which force field would fit well on this system?
2 - Should I develop new parameters? If so, how can I properly do it?

3 - I've heard that I should develop new parameters considering the excited
state of the fluorophore. Is it really needed?

I think that's all for now.

Thanks.


==



Gustavo Avelar Molina, B.Sc. Chem.

M.Sc. Chem. Student



Departamento de Química

Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto

Laboratório de Bioquímica e Biofísica de Proteínas

Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil



+55 16 994311221 | +55 11 949874141

avelarmolinagust...@gmail.com | gustavoavelarmol...@usp.br

https://lbbpusp.wordpress.com/o-grupo/membros/gustavo/ |

https://www.researchgate.net/profile/Gustavo_Avelar_Molina

==
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[gmx-users] Force field choosing and parameterization

2015-03-11 Thread Gustavo Avelar Molina

Hi,

I'm new here and I barely have experience in GROMACS. I'm seeking some help
to solve an issue.

I want to run MD simulations of an enzyme that:

1 - Have a fluorescent probe attached next to the catalytic site;
2 - Have a polysaccharide (substrate) embedded in its catalytic site;

One simulation with both conditions at the same time, another with just the
first. I don't know yet if I'll need to use a QM/MM method. Maybe you could
help me to decide it too.

The objective is to correlate the MD simulations results to other
experimental results, such as fluorescence spectroscopy of the same system,
since the fluorophore emission spectrum changes in the presence of
substrate. By knowing the probe environment changes due to the substrate
presence in comparison to the system without it, one could explain the
experimental data, and vice versa. What I want to know is:

1 - Which force field would fit well on this system?
2 - Should I develop new parameters? If so, how can I properly do it?
3 - I've heard that I should develop new parameters considering the excited
state of the fluorophore. Is it really needed?

I think that's all for now.

Thanks.


==



Gustavo Avelar Molina, B.Sc. Chem.

M.Sc. Chem. Student



Departamento de Química

Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto

Laboratório de Bioquímica e Biofísica de Proteínas

Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil



+55 16 994311221 | +55 11 949874141

avelarmolinagust...@gmail.com | gustavoavelarmol...@usp.br

https://lbbpusp.wordpress.com/o-grupo/membros/gustavo/ |

https://www.researchgate.net/profile/Gustavo_Avelar_Molina

==
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[gmx-users] g_anaeig error inconsistent shifts

2015-03-11 Thread tasneem kausar

for PCA i used the g_covar followed by g_anaeig.
i used the command line for g_covr as
g_covar -f full.xtc -s full.tpr -o eig.xvg
I have selected the protein for least square fit and main chain for
covarience analysis.
There is a warning message.
WARNING: number of atoms in tpx (312) and trajectory (1061) do not match

The above command generates the files average.pdb, eigenvec.trr and eig.xvg
Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
The commnan line for g_anaeig is given below.
g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
For least square fit i have selected the protein and same for the
eigenvectors
This gave the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?
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Re: [gmx-users] g_anaeig error inconsistent shifts

2015-03-11 Thread Tsjerk Wassenaar

Hi Tasneem,

So your tpr file doesn't match your trajectory. How come, or why is that?
And if your eigenvectors correspond to main chain atoms you can't use
protein for analysis.

Hope it helps,

Tsjerk
On Mar 12, 2015 6:07 AM, "tasneem kausar"  wrote:

> for PCA i used the g_covar followed by g_anaeig.
> i used the command line for g_covr as
> g_covar -f full.xtc -s full.tpr -o eig.xvg
> I have selected the protein for least square fit and main chain for
> covarience analysis.
> There is a warning message.
> WARNING: number of atoms in tpx (312) and trajectory (1061) do not match
>
> The above command generates the files average.pdb, eigenvec.trr and eig.xvg
> Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
> The commnan line for g_anaeig is given below.
> g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
> For least square fit i have selected the protein and same for the
> eigenvectors
> This gave the following message;
> There were 40 inconsistent shifts. Check your topology
> where is the problem occured?
> --
> Gromacs Users mailing list
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[gmx-users] trajectory film

2015-03-11 Thread mah maz

Dear all,
I have a question probably not related to this mailing list! I want to see
a film of an output trajectory via VMD. I tried the .trr file by the
appropriate format in VMD, it shows that the frames are being constructed
and rendering is complete but nothing can be seen. Is there a problem with
my .trr file? Can anyone help me in this regard?
thanks!
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Re: [gmx-users] Segmentation fault

2015-03-11 Thread Mark Abraham

Hi,

I would not expect a good result from using both wrapper compilers and a
collection of manually-specified include and library paths, because you
have good chances of getting some detail wrong. Getting those right is a
matter of following the docs for the MVAPICH2 + icc combination. In
particular, you likely want to have followed Intel's advice about sourcing
their compiler setup scripts.

Unrelated, but turning off OpenMP support seems likely to give away options
for improved performance for no real benefit.

Mark

On Thu, Mar 12, 2015 at 12:28 AM, Wim Rm Cardoen 
wrote:

> Hello,
>
> I have compiled the latest version of gromacs (5.0.4) on our cluster
> (RHEL6 OS)
> using the intel compiler (2015.1.133) as well as mvapich2 2.0 compiled
> with the same version of the INTEL compiler.
> For the FFTW and the BLAS/LAPACK I used Intel MKL's library.
> When I tested the regression test ALL tests failed due to segmentation
> faults at the MPI level.
> Help would be strongly appreciated.
>
> Thanks ,
>
> Wim
>
> I compiled gromacs 5.0.4 with the following flags (Non-threaded and
> non-gpu version)
> 
> cmake .. -DCMAKE_INSTALL_PREFIX=/uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i \
>
>  -DCMAKE_C_COMPILER=/uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpicc \
>
>  -DCMAKE_CXX_COMPILER=/uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpicxx \
>  -DCMAKE_INCLUDE_PATH="
> -I/uufs/ember.arches/sys/pkg/mvapich2/2.0i/include  -I/uufs/
> chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/mkl/include/fftw " \
>  -DCMAKE_LIBRARY_PATH="
> -Wl,-rpath=/uufs/ember.arches/sys/pkg/mvapich2/2.0i/lib
> -L/uufs/ember.arches/sys/pkg/mvapich2/2.0i/lib -lmpich  -Wl,-rpath=/uufs/
> chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/mkl/lib/intel64  -L/uufs/
> chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/mkl/lib/intel64
> -lmkl_core -lmkl_intel_lp64 -lmkl_sequential  -Wl,-rpath=/uufs/
> chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/lib/intel64  -L/uufs/
> chpc.utah.edu/sys/pkg/intel/ics/composer_xe_2015/lib/intel64 -limf
> -lifcore " \
>   -DGMX_MPI=on  -DGMX_DOUBLE=ON  -DGMX_FFT_LIBRARY=mkl
> -DGMX_BUILD_MANUAL=on \
>   -DGMX_OPENMP=OFF  -DGMX_THREAD_MPI=OFF
> make -j 6
> make check
> # 100% tests passed, 0 tests failed out of 15
> #
> # Label Time Summary:
> # GTest  =   5.77 sec
> # IntegrationTest=  24.73 sec
> # UnitTest   =   5.77 sec
>
> make install
>
>
> # Regression tests
> wget http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz
> tar -zxvf regressiontests-5.0.4.tar.gz<
> http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz>
> cd regressiontests-5.0.4
> module load intel/2015.1.133
> module load mvapich2/2.0.em.i
> source /uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/GMXRC
> which mdrun_mpi_d
> # /uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/mdrun_mpi_d
> which mpirun
> # /uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpirun
> ./gmxtest.pl -np 12 -verbose -double  -mdrun  /uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/mdrun_mpi_d
>  -mpirun /uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpirun simple
>
>
> #
> -
> Abnormal return value for
> '/uufs/ember.arches/sys/pkg/mvapich2/2.0i/bin/mpirun -np 12 -wdir /uufs/
> chpc.utah.edu/common/home/u0253283/regressiontests-5.0.4/simple/rb125
> /uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/mdrun_mpi_d
> -notunepme >mdrun.out 2>&1' was -1
> FAILED. Check mdrun.out, md.log file(s) in rb125 for rb125
> 16 out of 16 simple tests FAILED
>
> GROMACS:  gmx mdrun, VERSION 5.0.4 (double precision)
> Executable:   /uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/bin/gmx_mpi_d
> Library dir:  /uufs/
> chpc.utah.edu/sys/installdir/gromacs/5.0.4-mvapich2-2.0.em.i/share/gromacs/top
> Command line:
>   mdrun_mpi_d -notunepme
>
> Reading file topol.tpr, VERSION 5.0.4 (double precision)
> [em110:mpi_rank_0][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_1][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_3][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_4][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_9][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_2][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_5][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_6][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_rank_7][error_sighandler] Caught error: Segmentation fault
> (signal 11)
> [em110:mpi_ran

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