date:20171004

Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-04 Thread Christopher Neale

Please show us the plots (upload to a file hosting site and paste the link in 
your post) or precisely define your results; also explain precisely why the 
results are unexpected. Also show us your exact commands. Without this we can 
not help.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Dilip H N 

Sent: 04 October 2017 23:48:08
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

Hello,
I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent)
and water for different concentration (by varying composition of cosolvent:
water). I have used Charmm36 FF for TMAO.
Now if i am plotting the RDF for Amino acid v/s Water in the presence of
different concentrations TMAO, I am getting wired RDF's for each
composition of TMAO present, the peaks are absurd.
Why is this happening..?? i have looked into the final structure of my
simulation in VMD which is correct
I am confused...
Any Suggestions are appreciated...


--
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Constant Pressure just in z axis

2017-10-04 Thread Christopher Neale

Use semi-isotropic pressure coupling and use a water-type compressibility in 
the z dimension by a compressibility of 0 in the x/y dimension. That will give 
you precisely what you are looking for. We've used it before to simulate octane 
slabs as lipid bilayer mimetics and it work just fine.


Gromacs help pages list:

"compressibility (NOTE: this is now really in bar-1) For water at 1 atm and 300 
K the compressibility is 4.5e-5 [bar-1]"


so that is what I would use for the z dimension.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Iman 
Ahmadabadi 
Sent: 04 October 2017 11:17:38
To: gmx-us...@gromacs.org
Subject: [gmx-users] Constant Pressure just in z axis

Dear users,

I would like to keep the pressure (1 bar) in the z direction and there is
not any similar condition in X/Y directions, I mean it's not obligatory for
keeping the pressure in a specific value in X/Y direction. Is the
semiisotropic coupling sufficient to my purpose? If it is, which value
should I use for each X and X/Y directions for pressure coupling?

Respectfully,
Iman Ahmadabadi
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[gmx-users] How to recover a corrupted .edr file

2017-10-04 Thread Christopher Neale

Dear users:


I recently experienced some corruption in a .xtc and a .edr file. Recovering 
the .xtc was pretty easy, I use gmx trjconv -b and -e to get the part before 
the corruption and the part after the corruption, which was itself a small 
chunk. This presumably works because trjconv actually skips to the -b time 
without reading through to get there.


However, gmx eneconv seems to start reading always form the start of the .edr 
file. This is fine for a normal file, where it reads the initial frames through 
until the -b time and then starts writing to the output file. However, with a 
corrupted file, it causes problems because it hangs up on the corruption. To 
put it more planly, gmx trjconv fails with a corrupted .xtc but can recover a 
readable part beyond the corruption with a -b value just beyond the end of the 
corruption; this is not possible with my usage of gmx eneconv. I'm hoping that 
there is some alternative.


Below is what I get with gmx eneconv from version 5.1.2. I als tried 2016.2 and 
got the same result. You can see that it lists the start time as "0" ps even 
though I sent it -b 379000. This is not a bug, since I tested with a 
non-corrupted file and gmx eneconv will respect the -b flag in what it writes 
out. It's just that eneconv can not seem to skip right to the -b point whereas 
trjconv can.


GROMACS:  gmx eneconv, VERSION 5.1.2
Executable:   /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
Data prefix:  /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial
Command line:
  gmx eneconv -f 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr -b 379000 -o 
120LPL/DOPC_DPPC_chol_1_1_1_310K/MD_post_379000ps.edr

Opened 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr as single precision energy file
^MReading energy frame  0 time0.000 ^MReading energy frame  
1 time2.000
Sorting disabled.

Summary of files and start times used:

  FileStart time
-
120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr0.000

Opened 120LPL/DOPC_DPPC_chol_1_1_1_310K/MD.edr as single precision energy file
...



Thank you,
Chris.
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[gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-04 Thread Dilip H N

Hello,
I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent)
and water for different concentration (by varying composition of cosolvent:
water). I have used Charmm36 FF for TMAO.
Now if i am plotting the RDF for Amino acid v/s Water in the presence of
different concentrations TMAO, I am getting wired RDF's for each
composition of TMAO present, the peaks are absurd.
Why is this happening..?? i have looked into the final structure of my
simulation in VMD which is correct
I am confused...
Any Suggestions are appreciated...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

2017-10-04 Thread Dallas Warren

Done Mark, thanks.
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 4 October 2017 at 02:37, Mark Abraham  wrote:
> Hi,
>
> I'm sure we have opportunities to improve this code - please do file a
> redmine issue with repro inputs so we can profile and see!
>
> Thanks,
>
> Mark
>
> On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul  wrote:
>
>>
>>
>> On 10/2/17 11:14 PM, Dallas Warren wrote:
>> > Thanks for the reply Justin.
>> >
>> > I am just going to use the largest exclusion bond distance I can, then
>> > ignore the RDF of those beyond that distance.
>> >
>> > Seems curious to me (not actually understanding what grommp is
>> > generating) that the list is so large.  These are linear molecules, 38
>> > atoms, 60 molecules in total.
>>
>> It generates a matrix of all possible exclusions, sorts them, then removes
>> duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 *
>> 60 * (2
>> * sizeof(int)) - the factor of 2 for the atom numbers comes from the fact
>> that
>> you're actually allocating an array of type "sortable" which is a pair of
>> atom
>> numbers.
>>
>> -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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[gmx-users] problem of GB simulation

2017-10-04 Thread Albert


Hello,

I am using the following .mdp file for protein BG solvent simulations. 
However, the job always failed with the following messages:


vol -0.00! imb F 22% step 144100, remaining wall clock time: 207 s
vol -0.00! imb F 23% step 144200, remaining wall clock time:   207 s
vol -0.00! imb F 23% step 144300, remaining wall clock time:   207 s
vol -0.00! imb F 23% step 144400, remaining wall clock time:   207 s

---
Program gmx mdrun, VERSION 5.1.4
Source code file: 
/icm/home/albert/tmp/gromacs-5.1.4/src/gromacs/mdlib/nsgrid.c, line: 633


Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ind has value 131. It should have been within [ 0 .. 131 ]


The initial system seems to be all right since it is a liner peptide. 
The initial energy of the peptide is also very low. I am not so sure 
whether my .mdp is correct or not



Thank you very much.


define = -DREST_ON -DSTEP_NVT
integrator  = md
dt  = 0.001
nsteps  = 30
nstlog  = 1000

implicit_solvent = GBSA
gb_algorithm= OBC
;nstgbradii  = 1.0
rgbradii = 1.0
gb_epsilon_solvent = 80
gb_dielectric_offset= 0.009
sa_algorithm= ace-approximation
sa_surface_tension   = 0.0054
pbc= no
coulombtype = cut-off

cutoff-scheme   = group
nstlist = 20
rlist   = 1.0


tcoupl  = Nose-Hoover
tc_grps = Protein
tau_t   = 1.0
ref_t   = 310
;
constraints = h-bonds
constraint_algorithm= LINCS
;
nstcomm = 100
comm_mode   = angular
comm_grps   = Protein
;
gen-vel = yes
gen-temp= 310
gen-seed= -1
;
refcoord_scaling= com

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[gmx-users] Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

2017-10-04 Thread Robert König

Hi,
I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 2016.3. 
following the instructions on 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
I added TPO and SEP to aminoacids.rtp like:
[ TPO ] ; Phosphothreonine from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
 
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
 [ atoms ] ; !entry.THP.unit.atoms table
 N    N   -0.493700    1
 H    H    0.301800    2
    CA    CT  -0.1740  3
    HA    H1   0.016400    4
    CB    CT   0.15310 5
    HB    H1  -0.090900    6
   CG2    CT  -0.16170 7
  HG21    HC   0.049600    8
  HG22    HC   0.049600    9
  HG23    HC   0.049600   10
   OG1    OS  -0.637500   11
 P    P    1.400  12
   O1P    O2  -0.850  13
   O2P    O2  -0.850  14
   O3P    O2  -0.850  15
 C    C    0.673100   16
 O    O   -0.585400   17
 [ bonds ] ; !entry.THP.unit.connectivity table
 N H
 N    CA
    CA    HA
    CA    CB
    CA C
    CB    HB
    CB   CG2
    CB   OG1
   CG2  HG21
   CG2  HG22
   CG2  HG23
   OG1    PS
 S   O1P
 S   O2P
 S   O3P
 C O
    -C N   ; is present everywhere else
 [ impropers ] ; is present everywhere else
    -C    CA N H
    CA    +N C O

[ SEP ] ; Phosphoserine from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib
 
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
 [ atoms ] ; !entry.SEP.unit.atoms table
 N    N   -0.493700    1
 H    H    0.301800    2
    CA    CT  -0.238000    3
    HA    H1   0.093700    4
    CB    CT   0.078200    5
   HB2    H1  -0.060200    6
   HB3    H1  -0.060200    7
    OG    OS  -0.559300    8
 P    P    1.4 9
   O1P    O2  -0.850  10
   O2P    O2  -0.850  11
   O3P    O2  -0.850  12
 C    C    0.673100   13
 O    O   -0.585400   14
 [ bonds ] ; !entry.THP.unit.connectivity table
 N H
 N    CA
    CA    HA
    CA    CB
    CA C
    CB   HB2
    CB   HB3
    CB    OG
    OG    PS
 S   O1P
 S   O2P
 S   O3P
 C O
    -C N   ; is present everywhere else
 [ impropers ] ; is present everywhere else
    -C    CA N H
    CA    +N C O
My first question is, like I commented, on both entries the last four lines are 
not in the parameters I got from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
 and 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.libbut
 are found on all the other entries.So do I need these lines, are they right 
that way and what does it mean?

Second is in aminoacid.hdb.The entries look like:
"THR    5"
1    1    H    N    -C    CA    
1    5    HA    CA    N    CB    C    
1    5    HB    CB    CA    CG2    OG1    
3    4    HG2    CG2    CB    CA    
1    2    HG1    OG1    CB    CA
So I added till now:
TPO 4
1   H
1   HA 
1   HB
3   HG2
SEP 4
1   H
1   HA
1   HB2
1   HB3
is this right that far, especially TPO with 4 lines and 3 HG2?If somebody added 
these AA already I would be grateful for the missing parameters or a reliable 
source, I am not sure that my own estimations will be totally right.
Thanks a lot!
If you are still in good mood I would be very glad if you would a quick glance 
at my whole proceding. It is my first time to add residues and it would be good 
to know if I missed something or made a mistake.
I followed 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

1. I added the parameter like in my first question.2. See my second question.3. 
Nothing - I didn't introduce new atom types
4. Nothing - I didn't require new bonded types
5. I added:TPO      Protein
SEP      Proteinto residuetypes.dat6. Nothing - There is new special 
connectivity to other residues.
So is that everything I have to do and do you see any mistakes?
Thank you very much!Sincerly, olaf
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[gmx-users] WG: Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

2017-10-04 Thread Robert König

Hi,


I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 2016.3. 
following the instructions on 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
I added TPO and SEP to aminoacids.rtp like:
[ TPO ] ; Phosphothreonine from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
 
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
 [ atoms ] ; !entry.THP.unit.atoms table
 N    N   -0.493700    1
 H    H    0.301800    2
    CA    CT  -0.1740  3
    HA    H1   0.016400    4
    CB    CT   0.15310 5
    HB    H1  -0.090900    6
   CG2    CT  -0.16170 7
  HG21    HC   0.049600    8
  HG22    HC   0.049600    9
  HG23    HC   0.049600   10
   OG1    OS  -0.637500   11
 P    P    1.400  12
   O1P    O2  -0.850  13
   O2P    O2  -0.850  14
   O3P    O2  -0.850  15
 C    C    0.673100   16
 O    O   -0.585400   17
 [ bonds ] ; !entry.THP.unit.connectivity table
 N H
 N    CA
    CA    HA
    CA    CB
    CA C
    CB    HB
    CB   CG2
    CB   OG1
   CG2  HG21
   CG2  HG22
   CG2  HG23
   OG1    PS
 S   O1P
 S   O2P
 S   O3P
 C O
    -C N   ; is present everywhere else
 [ impropers ] ; is present everywhere else
    -C    CA N H
    CA    +N C O

[ SEP ] ; Phosphoserine from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib
 
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
 [ atoms ] ; !entry.SEP.unit.atoms table
 N    N   -0.493700    1
 H    H    0.301800    2
    CA    CT  -0.238000    3
    HA    H1   0.093700    4
    CB    CT   0.078200    5
   HB2    H1  -0.060200    6
   HB3    H1  -0.060200    7
    OG    OS  -0.559300    8
 P    P    1.4 9
   O1P    O2  -0.850  10
   O2P    O2  -0.850  11
   O3P    O2  -0.850  12
 C    C    0.673100   13
 O    O   -0.585400   14
 [ bonds ] ; !entry.THP.unit.connectivity table
 N H
 N    CA
    CA    HA
    CA    CB
    CA C
    CB   HB2
    CB   HB3
    CB    OG
    OG    PS
 S   O1P
 S   O2P
 S   O3P
 C O
    -C N   ; is present everywhere else
 [ impropers ] ; is present everywhere else
    -C    CA N H
    CA    +N C O
My first question is, like I commented, on both entries the last four lines are 
not in the parameters I got from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
 and 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.libbut
 are found on all the other entries.So do I need these lines, are they right 
that way and what does it mean?

Second is in aminoacid.hdb.The entries look like:
"THR    5"
1    1    H    N    -C    CA    
1    5    HA    CA    N    CB    C    
1    5    HB    CB    CA    CG2    OG1    
3    4    HG2    CG2    CB    CA    
1    2    HG1    OG1    CB    CA
So I added till now:
TPO 4
1   H
1   HA 
1   HB
3   HG2
SEP 4
1   H
1   HA
1   HB2
1   HB3
is this right that far, especially TPO with 4 lines and 3 HG2?If somebody added 
these AA already I would be grateful for the missing parameters or a reliable 
source, I am not sure that my own estimations will be totally right.
Thanks a lot!
If you are still in good mood I would be very glad if you would a quick glance 
at my whole proceding. It is my first time to add residues and it would be good 
to know if I missed something or made a mistake.
I followed 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

1. I added the parameter like in my first question.2. See my second question.3. 
Nothing - I didn't introduce new atom types
4. Nothing - I didn't require new bonded types
5. I added:TPO      Protein
SEP      Proteinto residuetypes.dat6. Nothing - There is new special 
connectivity to other residues.
So is that everything I have to do and do you see any mistakes?
Thank you very much!Sincerly, olaf
   
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Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Mark Abraham

Hi,

Depends which one... some of them extend the ensemble.

Mark

On Wed, Oct 4, 2017 at 5:36 PM Myunggi Yi  wrote:

> Peter,
>
> (ignoring full precision) Are the thermostat and barostat computed by
> coordinates and velocities, in principle ?
>
>
> Myunggi Yi  (이명기, Ph. D.), Professor
>
> Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of
> Engineering
> Interdisciplinary Program of Biomedical Mechanical & Electrical Engineering
> Center for Marine-Integrated Biomedical Technology (BK21+)
> College of Engineering
> Pukyong National University (부경대학교 www.pknu.ac.kr)
> 45 Yongso-ro, Nam-gu (남구 용소로 45)
> Busan, 48513, South Korea
> Phone: +82 51 629 5773 <+82%2051-629-5773>
> Fax: +82 51 629 5779 <+82%2051-629-5779>
>
> On Wed, Oct 4, 2017 at 11:07 AM, Peter Kroon  wrote:
>
> > Hi MY,
> >
> >
> > actually you lose continuity of your simulation in both cases. The cpt
> > file stores full precision coordinates and velocities (unlike gro/xtc).
> > In addition, it stores state information about the simulation itself,
> > such as the themostat and barostat. Whether this is an issue is up to
> > you of course ;)
> >
> >
> > Peter
> >
> >
> > On 04-10-17 16:24, Myunggi Yi wrote:
> > > 1. In principle, MD can be restarted if there are coordinates and
> > > velocities on the snapshot.
> > >
> > > 2. Even if you don't have velocity, you can assign random velocity with
> > the
> > > specific temperature.
> > > In this case, you lose continuity of simulation. Don't worry.
> > > If you run same simulation with the exactly same inputs (including the
> > same
> > > random seed), you won't get exactly same trajectory in most cases
> > > (depending on simulation types and hardware, etc).
> > >
> > > MY
> > >
> > >
> > > On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar 
> > wrote:
> > >
> > >> In that case, I think I do not have any option. The gmx_mpi_d check
> has
> > >> only the last frame. :(
> > >>
> > >> Command line:
> > >>   gmx_mpi_d check -f ../state.cpt
> > >>
> > >> Checking file ../state.cpt
> > >>
> > >> # Atoms  10703
> > >> Last frame -1 time 190772.080
> > >>
> > >>
> > >> Item#frames Timestep (ps)
> > >> Step 1
> > >> Time 1
> > >> Lambda   1
> > >> Coords   1
> > >> Velocities   1
> > >> Forces   0
> > >> Box  1
> > >>
> > >> Thanks for your replies. I appreciate it.
> > >>
> > >>
> > >> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul 
> wrote:
> > >>
> > >>>
> > >>> On 10/4/17 9:06 AM, tarak karmakar wrote:
> > >>>
> >  Hi Justin,
> >  Thanks for the quick reply.
> > 
> >  Is there any way to check if the frame is there in .cpt file or not?
> > 
> >  I did the following exercise at difference 'time=' values,
> >  gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr
> -time
> >  4 -o topol.tpr
> > 
> >  It seems in all the cases, the trajectory gets restarted from the
> last
> >  frame.
> > 
> > 
> > >>> The .cpt files are always overwritten unless you tell mdrun to keep
> > them.
> > >>> You can inspect the contents of any given .cpt file with gmx check.
> > >>>
> > >>> -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...@gromacs.org.
> > >>>
> > >>
> > >>
> > >> --
> > >> Regards,
> > >> Tarak
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at http://www.gromacs.org/
> > >> Support/Mailing_Lists/GMX-Users_List before posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> >

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Myunggi Yi

Peter,

(ignoring full precision) Are the thermostat and barostat computed by
coordinates and velocities, in principle ?


Myunggi Yi  (이명기, Ph. D.), Professor

Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of
Engineering
Interdisciplinary Program of Biomedical Mechanical & Electrical Engineering
Center for Marine-Integrated Biomedical Technology (BK21+)
College of Engineering
Pukyong National University (부경대학교 www.pknu.ac.kr)
45 Yongso-ro, Nam-gu (남구 용소로 45)
Busan, 48513, South Korea
Phone: +82 51 629 5773
Fax: +82 51 629 5779

On Wed, Oct 4, 2017 at 11:07 AM, Peter Kroon  wrote:

> Hi MY,
>
>
> actually you lose continuity of your simulation in both cases. The cpt
> file stores full precision coordinates and velocities (unlike gro/xtc).
> In addition, it stores state information about the simulation itself,
> such as the themostat and barostat. Whether this is an issue is up to
> you of course ;)
>
>
> Peter
>
>
> On 04-10-17 16:24, Myunggi Yi wrote:
> > 1. In principle, MD can be restarted if there are coordinates and
> > velocities on the snapshot.
> >
> > 2. Even if you don't have velocity, you can assign random velocity with
> the
> > specific temperature.
> > In this case, you lose continuity of simulation. Don't worry.
> > If you run same simulation with the exactly same inputs (including the
> same
> > random seed), you won't get exactly same trajectory in most cases
> > (depending on simulation types and hardware, etc).
> >
> > MY
> >
> >
> > On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar 
> wrote:
> >
> >> In that case, I think I do not have any option. The gmx_mpi_d check has
> >> only the last frame. :(
> >>
> >> Command line:
> >>   gmx_mpi_d check -f ../state.cpt
> >>
> >> Checking file ../state.cpt
> >>
> >> # Atoms  10703
> >> Last frame -1 time 190772.080
> >>
> >>
> >> Item#frames Timestep (ps)
> >> Step 1
> >> Time 1
> >> Lambda   1
> >> Coords   1
> >> Velocities   1
> >> Forces   0
> >> Box  1
> >>
> >> Thanks for your replies. I appreciate it.
> >>
> >>
> >> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul  wrote:
> >>
> >>>
> >>> On 10/4/17 9:06 AM, tarak karmakar wrote:
> >>>
>  Hi Justin,
>  Thanks for the quick reply.
> 
>  Is there any way to check if the frame is there in .cpt file or not?
> 
>  I did the following exercise at difference 'time=' values,
>  gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
>  4 -o topol.tpr
> 
>  It seems in all the cases, the trajectory gets restarted from the last
>  frame.
> 
> 
> >>> The .cpt files are always overwritten unless you tell mdrun to keep
> them.
> >>> You can inspect the contents of any given .cpt file with gmx check.
> >>>
> >>> -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...@gromacs.org.
> >>>
> >>
> >>
> >> --
> >> Regards,
> >> Tarak
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Myunggi Yi

Peter,

I see. Thank you for the correction.

MY
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[gmx-users] Constant Pressure just in z axis

2017-10-04 Thread Iman Ahmadabadi

Dear users,

I would like to keep the pressure (1 bar) in the z direction and there is
not any similar condition in X/Y directions, I mean it's not obligatory for
keeping the pressure in a specific value in X/Y direction. Is the
semiisotropic coupling sufficient to my purpose? If it is, which value
should I use for each X and X/Y directions for pressure coupling?

Respectfully,
Iman Ahmadabadi
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[gmx-users] gmx gpu error gmx: error libnvidia-ml.so.1

2017-10-04 Thread Syed Azeem

Hi all,

I tried installing Gromacs 2016.4 on a new hardware with Nvidia Quadro
K420 2gb support.

Installation completed successfully following Quick and Dirty method.
But gmx is not working.

Error says:

gmx: error while loading shared libraries: libnvidia-ml.so.1: cannot
open shared object file: No such file or directory

My cmake command:

cmake '/home/tt635kkb/Documents/gromacs-2016.4'
-DGMX_BUILD_OWN_FFTW=ON -DGMX_SIMD=AVX2_256 -DGMX_GPU=on
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0

For the toolkit, I did runfile installation from Nvidia.

Please help me out with the error

Thanks in advance

Azeem
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Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Peter Kroon

Hi MY,


actually you lose continuity of your simulation in both cases. The cpt
file stores full precision coordinates and velocities (unlike gro/xtc).
In addition, it stores state information about the simulation itself,
such as the themostat and barostat. Whether this is an issue is up to
you of course ;)


Peter


On 04-10-17 16:24, Myunggi Yi wrote:
> 1. In principle, MD can be restarted if there are coordinates and
> velocities on the snapshot.
>
> 2. Even if you don't have velocity, you can assign random velocity with the
> specific temperature.
> In this case, you lose continuity of simulation. Don't worry.
> If you run same simulation with the exactly same inputs (including the same
> random seed), you won't get exactly same trajectory in most cases
> (depending on simulation types and hardware, etc).
>
> MY
>
>
> On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar  wrote:
>
>> In that case, I think I do not have any option. The gmx_mpi_d check has
>> only the last frame. :(
>>
>> Command line:
>>   gmx_mpi_d check -f ../state.cpt
>>
>> Checking file ../state.cpt
>>
>> # Atoms  10703
>> Last frame -1 time 190772.080
>>
>>
>> Item#frames Timestep (ps)
>> Step 1
>> Time 1
>> Lambda   1
>> Coords   1
>> Velocities   1
>> Forces   0
>> Box  1
>>
>> Thanks for your replies. I appreciate it.
>>
>>
>> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul  wrote:
>>
>>>
>>> On 10/4/17 9:06 AM, tarak karmakar wrote:
>>>
 Hi Justin,
 Thanks for the quick reply.

 Is there any way to check if the frame is there in .cpt file or not?

 I did the following exercise at difference 'time=' values,
 gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
 4 -o topol.tpr

 It seems in all the cases, the trajectory gets restarted from the last
 frame.


>>> The .cpt files are always overwritten unless you tell mdrun to keep them.
>>> You can inspect the contents of any given .cpt file with gmx check.
>>>
>>> -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...@gromacs.org.
>>>
>>
>>
>> --
>> Regards,
>> Tarak
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>


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Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Myunggi Yi

1. In principle, MD can be restarted if there are coordinates and
velocities on the snapshot.

2. Even if you don't have velocity, you can assign random velocity with the
specific temperature.
In this case, you lose continuity of simulation. Don't worry.
If you run same simulation with the exactly same inputs (including the same
random seed), you won't get exactly same trajectory in most cases
(depending on simulation types and hardware, etc).

MY


On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar  wrote:

> In that case, I think I do not have any option. The gmx_mpi_d check has
> only the last frame. :(
>
> Command line:
>   gmx_mpi_d check -f ../state.cpt
>
> Checking file ../state.cpt
>
> # Atoms  10703
> Last frame -1 time 190772.080
>
>
> Item#frames Timestep (ps)
> Step 1
> Time 1
> Lambda   1
> Coords   1
> Velocities   1
> Forces   0
> Box  1
>
> Thanks for your replies. I appreciate it.
>
>
> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 10/4/17 9:06 AM, tarak karmakar wrote:
> >
> >> Hi Justin,
> >> Thanks for the quick reply.
> >>
> >> Is there any way to check if the frame is there in .cpt file or not?
> >>
> >> I did the following exercise at difference 'time=' values,
> >> gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
> >> 4 -o topol.tpr
> >>
> >> It seems in all the cases, the trajectory gets restarted from the last
> >> frame.
> >>
> >>
> > The .cpt files are always overwritten unless you tell mdrun to keep them.
> > You can inspect the contents of any given .cpt file with gmx check.
> >
> > -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...@gromacs.org.
> >
>
>
>
> --
> Regards,
> Tarak
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread tarak karmakar

In that case, I think I do not have any option. The gmx_mpi_d check has
only the last frame. :(

Command line:
  gmx_mpi_d check -f ../state.cpt

Checking file ../state.cpt

# Atoms  10703
Last frame -1 time 190772.080


Item#frames Timestep (ps)
Step 1
Time 1
Lambda   1
Coords   1
Velocities   1
Forces   0
Box  1

Thanks for your replies. I appreciate it.


On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul  wrote:

>
>
> On 10/4/17 9:06 AM, tarak karmakar wrote:
>
>> Hi Justin,
>> Thanks for the quick reply.
>>
>> Is there any way to check if the frame is there in .cpt file or not?
>>
>> I did the following exercise at difference 'time=' values,
>> gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
>> 4 -o topol.tpr
>>
>> It seems in all the cases, the trajectory gets restarted from the last
>> frame.
>>
>>
> The .cpt files are always overwritten unless you tell mdrun to keep them.
> You can inspect the contents of any given .cpt file with gmx check.
>
> -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...@gromacs.org.
>



-- 
Regards,
Tarak
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Re: [gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Justin Lemkul




On 10/4/17 9:06 AM, tarak karmakar wrote:

Hi Justin,
Thanks for the quick reply.

Is there any way to check if the frame is there in .cpt file or not?

I did the following exercise at difference 'time=' values,
gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
4 -o topol.tpr

It seems in all the cases, the trajectory gets restarted from the last
frame.



The .cpt files are always overwritten unless you tell mdrun to keep them. You 
can inspect the contents of any given .cpt file with gmx check.


-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] CHARMM2GMX

2017-10-04 Thread Justin Lemkul




On 10/4/17 8:36 AM, Sergio Manzetti wrote:

Hi, after installing nt, I get:

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov 19 
2016, 06:48:10)
[GCC 5.4.0 20160609]

NOTE2: Please be sure to use the same version of CGenFF in your simulations 
that was used during parameter generation:
--Version of CGenFF detected in pfos.str : 3.0.1

WARNING: CGenFF versions are not equivalent!


ERROR: Could not detect CGenFF version. Exiting.



Comment out the version check. If you have further problems using the script, 
just contact me as this is not a GROMACS issue.


-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
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[gmx-users] CHARMM2GMX

2017-10-04 Thread Sergio Manzetti

Hi, after installing nt, I get: 

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov 19 
2016, 06:48:10) 
[GCC 5.4.0 20160609] 

NOTE2: Please be sure to use the same version of CGenFF in your simulations 
that was used during parameter generation: 
--Version of CGenFF detected in pfos.str : 3.0.1 

WARNING: CGenFF versions are not equivalent! 


ERROR: Could not detect CGenFF version. Exiting. 








Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] peptide ligand

2017-10-04 Thread ‪farial tavakoli‬ ‪

Dear Justin
Thank you so much for all of your help
best 
Farial

  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Wednesday, 4 October 2017, 15:19:38
 Subject: Re: [gmx-users] peptide ligand

On 10/3/17 1:51 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Because in tuturial , energygroups = protein JZ4So I think ,I 
>have to seperate my ligand and Protein in .mdp files and determine H bonds?
> 

It has nothing to do with the .mdp file. If you want to analyze hydrogen bonds, 
then you can create an .ndx file later for use with gmx hbond.

-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
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Re: [gmx-users] ERROR in cgenff_charmm2gmx.py

2017-10-04 Thread Sergio Manzetti

Cheers 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, October 4, 2017 1:50:08 PM 
Subject: Re: [gmx-users] ERROR in cgenff_charmm2gmx.py 

On 10/4/17 7:11 AM, Sergio Manzetti wrote: 
> Hi Justin, can [ 
> http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py
>  | cgenff_charmm2gmx.py ] do full charges? I get an error: 
> 
> Traceback (most recent call last): 
> File "./charmm2gmx.py", line 47, in  
> import networkx as nx 
> ImportError: No module named networkx 
> 

That's a Python dependency. Install it. 

-Justin 

> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "sergio manzetti"  
> To: "gmx-users"  
> Sent: Wednesday, October 4, 2017 1:07:20 PM 
> Subject: Re: [gmx-users] Topolgen and topolbuild 
> 
> Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated 
> molecule? 
> 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Wednesday, October 4, 2017 12:41:50 PM 
> Subject: Re: [gmx-users] Topolgen and topolbuild 
> 
> On 10/4/17 6:09 AM, Sergio Manzetti wrote: 
>> Hi Stephane. Thanks for that. I have tried it, however it generates a str 
>> file, and from there how to generate the GMX ITP is unknown. 
>> 
>> Is there a tutorial that shows how to generate ITP from STR? 
> 
> Use our conversion script: 
> 
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs 
> 
> -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] CR atom name CHARMM27 ff

2017-10-04 Thread Justin Lemkul




On 10/4/17 7:30 AM, Sergio Manzetti wrote:

Hi , I have tried to convert the mol2 to ITP by protparam.org, and apparently 
it works, nevertheless it gives a CR atom for alkane carbons. This CR is not in 
the charm27 ff atomtypes. What is the correct name for this?



If you're getting a force field file that has atomtypes that are not present in 
the parent force field, you should immediately be suspicious of compatibility. 
CR is indeed not a normal CHARMM atom type. I don't know what "protparam.org" is 
(and that website doesn't load anything for me) but whatever you're using needs 
to clearly explain what it's doing to generate parameters.


If you want to be safe in generating CHARMM topologies, use cgenff.paramchem.org 
- it is 100% compatible with the latest CHARMM36 force field and always provides 
all necessary parameters, as well as clear indications of areas needing 
refinement in the topology. That, to me, is the gold standard of parametrization.


-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] ERROR in cgenff_charmm2gmx.py

2017-10-04 Thread Justin Lemkul




On 10/4/17 7:11 AM, Sergio Manzetti wrote:

Hi Justin, can [ 
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py
 | cgenff_charmm2gmx.py ] do full charges? I get an error:

Traceback (most recent call last):
File "./charmm2gmx.py", line 47, in 
import networkx as nx
ImportError: No module named networkx



That's a Python dependency. Install it.

-Justin




Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "sergio manzetti" 
To: "gmx-users" 
Sent: Wednesday, October 4, 2017 1:07:20 PM
Subject: Re: [gmx-users] Topolgen and topolbuild

Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated 
molecule?



Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory 
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Wednesday, October 4, 2017 12:41:50 PM
Subject: Re: [gmx-users] Topolgen and topolbuild

On 10/4/17 6:09 AM, Sergio Manzetti wrote:

Hi Stephane. Thanks for that. I have tried it, however it generates a str file, 
and from there how to generate the GMX ITP is unknown.

Is there a tutorial that shows how to generate ITP from STR?


Use our conversion script:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

-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] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread Justin Lemkul




On 10/4/17 6:26 AM, tarak karmakar wrote:

Hi All,
Is there any way to continue a simulation from an intermediate time scale,
(say, from a frame at time=180 ns instead of 190.772 ns)?



Only if you have the .cpt file that corresponds to that frame.

-Justin


gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
18 -o topol.tpr
gmx_mpi_d mdrun -s topol.tpr -noappend

This does not help as it restarts from the last frame as saved in state.cpt
file.


-
Started mdrun on rank 0 Tue Oct  3 16:15:35 2017
Step   Time Lambda
95386040   190772.080000.0

-

I appreciate any help.



--
==

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] checking simulation time

2017-10-04 Thread Justin Lemkul




On 10/4/17 3:22 AM, Bukunmi Akinwunmi wrote:

thanks Justin and Tasneem. but how do i retrieve the log file from an ongoing 
simulation. all I have is the job id because I am using a cluster for the 
calculation.



Well, the output is being written somewhere, so that's where you go looking.

-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] peptide ligand

2017-10-04 Thread Justin Lemkul




On 10/3/17 1:51 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Because in tuturial , energygroups = protein JZ4So I think ,I 
have to seperate my ligand and Protein in .mdp files and determine H bonds?



It has nothing to do with the .mdp file. If you want to analyze hydrogen bonds, 
then you can create an .ndx file later for use with gmx hbond.


-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] peptide ligand

2017-10-04 Thread Justin Lemkul




On 10/3/17 1:46 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Oh I am sorry. Yes  I am trying to run md on my protein peptide 
complex. At first you advice me to use pdb2gmx to generate a topology for my 
complex and  I did. Then  according to the protein ligand complex tuturial in 
gromacs, I defined newbox and solvate After adding ions, I need to do energy 
minimization and use .mdp file which I should specify energygrouos , But my 
protein and ligand are not sepearate from each other. I just eant to know isnt 
there any problem if protein and ligand are merged and not separated?


The use of energygrps may or may not even be useful. It's not necessary for 
actually doing the simulation and you can always look at it later with mdrun -rerun.


-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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[gmx-users] CR atom name CHARMM27 ff

2017-10-04 Thread Sergio Manzetti

Hi , I have tried to convert the mol2 to ITP by protparam.org, and apparently 
it works, nevertheless it gives a CR atom for alkane carbons. This CR is not in 
the charm27 ff atomtypes. What is the correct name for this? 

Thanks 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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[gmx-users] ERROR in cgenff_charmm2gmx.py

2017-10-04 Thread Sergio Manzetti

Hi Justin, can [ 
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py
 | cgenff_charmm2gmx.py ] do full charges? I get an error: 

Traceback (most recent call last): 
File "./charmm2gmx.py", line 47, in  
import networkx as nx 
ImportError: No module named networkx 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "sergio manzetti"  
To: "gmx-users"  
Sent: Wednesday, October 4, 2017 1:07:20 PM 
Subject: Re: [gmx-users] Topolgen and topolbuild 

Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated 
molecule? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory 
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, October 4, 2017 12:41:50 PM 
Subject: Re: [gmx-users] Topolgen and topolbuild 

On 10/4/17 6:09 AM, Sergio Manzetti wrote: 
> Hi Stephane. Thanks for that. I have tried it, however it generates a str 
> file, and from there how to generate the GMX ITP is unknown. 
> 
> Is there a tutorial that shows how to generate ITP from STR? 

Use our conversion script: 

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs 

-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] Topolgen and topolbuild

2017-10-04 Thread Sergio Manzetti

Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated 
molecule? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, October 4, 2017 12:41:50 PM 
Subject: Re: [gmx-users] Topolgen and topolbuild 

On 10/4/17 6:09 AM, Sergio Manzetti wrote: 
> Hi Stephane. Thanks for that. I have tried it, however it generates a str 
> file, and from there how to generate the GMX ITP is unknown. 
> 
> Is there a tutorial that shows how to generate ITP from STR? 

Use our conversion script: 

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs 

-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] Topolgen and topolbuild

2017-10-04 Thread Justin Lemkul




On 10/4/17 6:09 AM, Sergio Manzetti wrote:

Hi Stephane. Thanks for that. I have tried it, however it generates a str file, 
and from there how to generate the GMX ITP is unknown.

Is there a tutorial that shows how to generate ITP from STR?


Use our conversion script:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

-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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[gmx-users] continue simulation from intermediate frame instead of last frame

2017-10-04 Thread tarak karmakar

Hi All,
Is there any way to continue a simulation from an intermediate time scale,
(say, from a frame at time=180 ns instead of 190.772 ns)?

gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
18 -o topol.tpr
gmx_mpi_d mdrun -s topol.tpr -noappend

This does not help as it restarts from the last frame as saved in state.cpt
file.


-
Started mdrun on rank 0 Tue Oct  3 16:15:35 2017
   Step   Time Lambda
   95386040   190772.080000.0

-

I appreciate any help.

-- 
Regards,
Tarak
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[gmx-users] Generate GROMACS topology

2017-10-04 Thread Sergio Manzetti

PS: For those silent wonderers on this topic, SWISSPARAM can do the trick: 

https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=24554 



Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] Topolgen and topolbuild

2017-10-04 Thread Sergio Manzetti

PS: generate ITP from STR without CHARMM GUI 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "ABEL Stephane"  
To: "gromacs org gmx-users"  
Sent: Wednesday, October 4, 2017 12:15:19 PM 
Subject: [gmx-users] Topolgen and topolbuild 

Hi 

if your molecule is a ligand, you could use ParamChem 
(https://cgenff.paramchem.org/) 

Stéphane 

-- 

Message: 1 
Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) 
From: Sergio Manzetti  
To: gmx-users  
Subject: [gmx-users] Topolgen and topolbuild 
Message-ID: 
<1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no> 
Content-Type: text/plain; charset=utf-8 

Hi, I found these tow programs on GMX site, however they don't work. How can I 
generate a CHARMM topology to be used in GMX for a charged molecule? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | 
Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | 
FAP ] 
-- 
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Re: [gmx-users] Topolgen and topolbuild

2017-10-04 Thread Sergio Manzetti

Hi Stephane. Thanks for that. I have tried it, however it generates a str file, 
and from there how to generate the GMX ITP is unknown. 

Is there a tutorial that shows how to generate ITP from STR? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "ABEL Stephane"  
To: "gromacs org gmx-users"  
Sent: Wednesday, October 4, 2017 12:15:19 PM 
Subject: [gmx-users] Topolgen and topolbuild 

Hi 

if your molecule is a ligand, you could use ParamChem 
(https://cgenff.paramchem.org/) 

Stéphane 

-- 

Message: 1 
Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) 
From: Sergio Manzetti  
To: gmx-users  
Subject: [gmx-users] Topolgen and topolbuild 
Message-ID: 
<1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no> 
Content-Type: text/plain; charset=utf-8 

Hi, I found these tow programs on GMX site, however they don't work. How can I 
generate a CHARMM topology to be used in GMX for a charged molecule? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | 
Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | 
FAP ] 
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[gmx-users] Topolgen and topolbuild

2017-10-04 Thread ABEL Stephane

Hi

if your molecule is a ligand, you could use ParamChem 
(https://cgenff.paramchem.org/) 

Stéphane

--

Message: 1
Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST)
From: Sergio Manzetti 
To: gmx-users 
Subject: [gmx-users] Topolgen and topolbuild
Message-ID:
<1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no>
Content-Type: text/plain; charset=utf-8

Hi, I found these tow programs on GMX site, however they don't work. How can I 
generate a CHARMM topology to be used in GMX for a charged molecule?

Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | 
Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | 
FAP ]
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[gmx-users] force field for acetylated protein pdb file

2017-10-04 Thread Raag Saluja

Hi!

I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need
to simulate it using GROMACS. Which force field would be the best for this
purpose?

Thank you in advance!

Regards,
Raag
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[gmx-users] Topolgen and topolbuild

2017-10-04 Thread Sergio Manzetti

Hi, I found these tow programs on GMX site, however they don't work. How can I 
generate a CHARMM topology to be used in GMX for a charged molecule? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] C++ xtc interface

2017-10-04 Thread David van der Spoel


On 02/10/17 23:16, Adriaan Riet wrote:

Hello,

I would like to do some work with xtc output files, but I'm having trouble.
The documentation  has the
following functions:

/* All functions return 1 if successful, 0 otherwise */

extern int open_xtc(XDR *xd,char *filename,char *mode);
/* Open a file for xdr I/O */

extern void close_xtc(XDR *xd);
/* Close the file for xdr I/O */

extern int read_first_xtc(XDR *xd,char *filename,
  int *natoms,int *step,real *time,
  matrix box,rvec **x,real *prec);


while the header file exposes the following signatures:

struct t_fileio *open_xtc(const char *filename, const char *mode);
/* Open a file for xdr I/O */

void close_xtc(struct t_fileio *fio);
/* Close the file for xdr I/O */

int read_first_xtc(struct t_fileio *fio,
int *natoms, gmx_int64_t *step, real *time,
matrix box, rvec **x, real *prec, gmx_bool *bOK);
/* Open xtc file, read xtc file first time, allocate memory for x */

Further, the documentation mentions that you should link to -lgmx, but the
only library I see for gromacs >=5.1 is -lgromacs (or -lgromacs_d). I
assumed the function signature of the header file was correct, and made a
small test case:

#include
#include "gromacs/fileio/xtcio.h"
int main(int argc, char* argv[]){
   const char
filename[]={"$HOME/Documents/Research/gromacs/oakley/june2017Test/2017/09-21/10-06_angle0.42impConc0T1873.xtc"};
   const char mode[]={'r'};
   t_fileio *xdrFile = open_xtc(filename,mode);
   int *natoms;
   gmx_int64_t *step;
   real *time;
   matrix box;
   rvec **x;
   real *prec;
   gmx_bool *bOK;
   int answer=read_first_xtc(xdrFile,natoms,step,time,box,x,prec,bOK);
   std::cout<

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