Re: [gmx-users] Number of interactions per residue

[Kavyashree M]

Dear users,

*When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -*
I get the following message -
***
Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 509 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 509 to 509
- Reduced number of distances from 0 to 0
Average number of contacts per timeframe 0.000 out of 112338 possible

---
Program g_hbond, VERSION 4.5.3
Source code file: gmx_hbond.c, line: 4052

Range checking error:
Variable y has value 0. It should have been within [ 0 .. 0 ]

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

*With the option -contact -r2 0.4 on C-alpha atoms I get-*

Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507

*With the option -contact -r 0.35 -r2 0.4 on C-alpha atoms I get-*

Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507

The index and the matrix that it writes has only 4 contacts (highlighted).
Why is it says as Hbond?
But isnt the "507" the number of contacts?
What is the 4 hbonds?

What do I need to do If I want to get the C-alpha contacts in the form
of a matrix, which gives the presence/absence of a contact over the
entire simulation?

Kindly help..

Thank you
Kavya

On Tue, Feb 19, 2013 at 9:56 AM, Kavyashree M  wrote:

> Sir,
>
> My purpose was to compare two simulations of the
> same protein at different temperatures. So I wanted
> to see how the interaction of each residue with other
> residues, within a cut-off, varies between the two.
> by using the matrix of C-alpha contact over the whole
> trajectory.
>
> Thank you
> kavya
>
>
> On Tue, Feb 19, 2013 at 9:50 AM, Kavyashree M  wrote:
>
>> Hello Sir,
>>
>> I used C-alpha atoms.
>>
>> Kavya
>>
>>
>> On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund wrote:
>>
>>> Hi,
>>>
>>> With -r2 one can provide a second, larger, cutoff so that contact
>>> kinetics can be analyzed within the Luzar-Chandler framework that were
>>> designed for hbonds.
>>>
>>> What index groups did you use?
>>>
>>> Erik
>>>
>>>
>>> On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote:
>>>
>>>  Dear users,

 As Suggested by Erik, I used g_hbond with -contact  to obtain a matrix
 of
 each contact as a function of time. I used the following command -
 g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400
 -hbn
 c.ndx

 I get only three contacts in the index file. The protein is a dimer of
 474
 residues
 (237 each). With a distance cut off of 0.5nm there should have been more
 number
 of contacts. And what is the difference in using -r only or -r2 only and
 combining -r
 and -r2?

 Thank you
 Kavya

 On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M 
 wrote:

  Thank you!
>
>
> On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund  >wrote:
>
>  Perhaps g_hbond -contact will do what you want.
>>
>> Erik
>>
>>
>> On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
>>
>> Dear users,
>>
>>>
>>> How can I get the number of interactions of each residue
>>> within a cut off as a function of time. just like g_saltbr writes
>>> with the option -sep.
>>> I tried using g_mdmat but it gives an average contact map.
>>>
>>> Thank you
>>> Kavya
>>> -- gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before

[gmx-users] There was 1 error in input file(s)

[라지브간디]

Dear GMX users,


I have done nvt part and then start to do npt part for my protein but it shows 
error like


Fatal error:
There was 1 error in input file(s)


Please how can avoid this? -- 
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[gmx-users] vaccum simulation error

[Rajalakshmi.C]

hi all,
i am trying to simulate polymer chains in solvent and vacuum media using 45a3
forcefield. for vacuum simulation i used different md parameters than that of
solvent media. first i put 100ps NVT and then 100ps NPT. i sucessfully got NVT
done but for NPT i got following error ,

WARNING 1 [file npt-pr.mdp, line unknown]:
  Turning off pressure coupling for vacuum system


NOTE 1 [file npt-pr.mdp, line unknown]:
  Tumbling and or flying ice-cubes: We are not removing rotation around
  center of mass in a non-periodic system. You should probably set
  comm_mode = ANGULAR.

Too many warnings (1), grompp_mpicc terminated.
If you are sure all warnings are harmless, use the -maxwarn option.

the parameters for NPT are;
nstlist  = 10
ns-type  = simple
pbc  = no
rlist= 0
coulombtype  = cut-off
rcoulomb = 0
fourierspacing   = 0.12
vdw-type = cut-off
pme_order= 4
rvdw = 0
ewald_rtol   = 0.1
Tcoupl   = v-rescale
tc-grps  = PMH  
tau_t= 0.1  
ref_t= 300
Pcoupl   = Berendsen
Pcoupltype   = Isotropic
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
DispCorr = no

can anyone suggest the solution for this vacuum simulation  
thanks in advance


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Re: [gmx-users] Number of interactions per residue

[Erik Marklund]

Try a more recent versions. There were a bunch of bugfixes since 4.5.3

Erik

On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote:


Dear users,

*When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -*
I get the following message -
***
Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 509 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 509 to 509
- Reduced number of distances from 0 to 0
Average number of contacts per timeframe 0.000 out of 112338 possible

---
Program g_hbond, VERSION 4.5.3
Source code file: gmx_hbond.c, line: 4052

Range checking error:
Variable y has value 0. It should have been within [ 0 .. 0 ]

For more information and tips for troubleshooting, please check the  
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
***

*With the option -contact -r2 0.4 on C-alpha atoms I get-*

Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507

*With the option -contact -r 0.35 -r2 0.4 on C-alpha atoms I get-*

Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507

The index and the matrix that it writes has only 4 contacts  
(highlighted).

Why is it says as Hbond?
But isnt the "507" the number of contacts?
What is the 4 hbonds?

What do I need to do If I want to get the C-alpha contacts in the form
of a matrix, which gives the presence/absence of a contact over the
entire simulation?

Kindly help..

Thank you
Kavya

On Tue, Feb 19, 2013 at 9:56 AM, Kavyashree M   
wrote:



Sir,

My purpose was to compare two simulations of the
same protein at different temperatures. So I wanted
to see how the interaction of each residue with other
residues, within a cut-off, varies between the two.
by using the matrix of C-alpha contact over the whole
trajectory.

Thank you
kavya


On Tue, Feb 19, 2013 at 9:50 AM, Kavyashree M   
wrote:



Hello Sir,

I used C-alpha atoms.

Kavya


On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund >wrote:



Hi,

With -r2 one can provide a second, larger, cutoff so that contact
kinetics can be analyzed within the Luzar-Chandler framework that  
were

designed for hbonds.

What index groups did you use?

Erik


On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote:

Dear users,


As Suggested by Erik, I used g_hbond with -contact  to obtain a  
matrix

of
each contact as a function of time. I used the following command -
g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e  
4400

-hbn
c.ndx

I get only three contacts in the index file. The protein is a  
dimer of

474
residues
(237 each). With a distance cut off of 0.5nm there should have  
been more

number
of contacts. And what is the difference in using -r only or -r2  
only and

combining -r
and -r2?

Thank you
Kavya

On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M 
wrote:

Thank you!



On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund 
wrote:


Perhaps g_hbond -contact will do what you want.


Erik


On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:

Dear users,



How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr  
writes

with the option -sep.
I tried using g_mdmat but it gives an average contact map.

Thank you
Kavya
-- gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users 
>



* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search**
Mailing_Lists/Search>before

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Re: [gmx-users] Number of interactions per residue

[Erik Marklund]

On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote:


Dear users,

*When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -*
I get the following message -
***
Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 509 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 509 to 509
- Reduced number of distances from 0 to 0
Average number of contacts per timeframe 0.000 out of 112338 possible

---
Program g_hbond, VERSION 4.5.3
Source code file: gmx_hbond.c, line: 4052

Range checking error:
Variable y has value 0. It should have been within [ 0 .. 0 ]

For more information and tips for troubleshooting, please check the  
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
***

*With the option -contact -r2 0.4 on C-alpha atoms I get-*

Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507

*With the option -contact -r 0.35 -r2 0.4 on C-alpha atoms I get-*

Reading frame   0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507

The index and the matrix that it writes has only 4 contacts  
(highlighted).

Why is it says as Hbond?


That should read 'contacts'


But isnt the "507" the number of contacts?


contacts within r2


What is the 4 hbonds?

What do I need to do If I want to get the C-alpha contacts in the form
of a matrix, which gives the presence/absence of a contact over the
entire simulation?

Kindly help..

Thank you
Kavya

On Tue, Feb 19, 2013 at 9:56 AM, Kavyashree M   
wrote:



Sir,

My purpose was to compare two simulations of the
same protein at different temperatures. So I wanted
to see how the interaction of each residue with other
residues, within a cut-off, varies between the two.
by using the matrix of C-alpha contact over the whole
trajectory.

Thank you
kavya


On Tue, Feb 19, 2013 at 9:50 AM, Kavyashree M   
wrote:



Hello Sir,

I used C-alpha atoms.

Kavya


On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund >wrote:



Hi,

With -r2 one can provide a second, larger, cutoff so that contact
kinetics can be analyzed within the Luzar-Chandler framework that  
were

designed for hbonds.

What index groups did you use?

Erik


On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote:

Dear users,


As Suggested by Erik, I used g_hbond with -contact  to obtain a  
matrix

of
each contact as a function of time. I used the following command -
g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e  
4400

-hbn
c.ndx

I get only three contacts in the index file. The protein is a  
dimer of

474
residues
(237 each). With a distance cut off of 0.5nm there should have  
been more

number
of contacts. And what is the difference in using -r only or -r2  
only and

combining -r
and -r2?

Thank you
Kavya

On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M 
wrote:

Thank you!



On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund 
wrote:


Perhaps g_hbond -contact will do what you want.


Erik


On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:

Dear users,



How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr  
writes

with the option -sep.
I tried using g_mdmat but it gives an average contact map.

Thank you
Kavya
-- gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users 
>



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Support/Mailing_Lists/Search**
Mailing_Lists/Search>before

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Re: [gmx-users] vaccum simulation error

[Erik Marklund]

Using a barostat for vaccum simulations is very peculiar.

Erik

On Feb 19, 2013, at 10:55 AM, Rajalakshmi.C wrote:



hi all,
i am trying to simulate polymer chains in solvent and vacuum media  
using 45a3
forcefield. for vacuum simulation i used different md parameters  
than that of
solvent media. first i put 100ps NVT and then 100ps NPT. i  
sucessfully got NVT

done but for NPT i got following error ,

WARNING 1 [file npt-pr.mdp, line unknown]:
 Turning off pressure coupling for vacuum system


NOTE 1 [file npt-pr.mdp, line unknown]:
 Tumbling and or flying ice-cubes: We are not removing rotation around
 center of mass in a non-periodic system. You should probably set
 comm_mode = ANGULAR.

Too many warnings (1), grompp_mpicc terminated.
If you are sure all warnings are harmless, use the -maxwarn option.

the parameters for NPT are;
nstlist  = 10
ns-type  = simple
pbc  = no
rlist= 0
coulombtype  = cut-off
rcoulomb = 0
fourierspacing   = 0.12
vdw-type = cut-off
pme_order= 4
rvdw = 0
ewald_rtol   = 0.1
Tcoupl   = v-rescale
tc-grps  = PMH  
tau_t= 0.1  
ref_t= 300
Pcoupl   = Berendsen
Pcoupltype   = Isotropic
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
DispCorr = no

can anyone suggest the solution for this vacuum simulation
thanks in advance


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[gmx-users] Re: vaccum simulation error

[raji]

for vacuum simulation , no need to specify cut-offs right. am using 8x8x8 box
and if we don't specify barostat it will again be a NVT simulations right.
vacuum simulations can be done only in NVT ??
sorry if am wrong . please clarify this doubt
thanks in advance



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Re: [gmx-users] Re: vaccum simulation error

[Felipe Pineda, PhD]

Have you maybe tried this?

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search?q=%22vacuum+simulation%22

Own initiative and discrete thinking is mandatory for research.

On 02/19/2013 12:32 PM, raji wrote:

for vacuum simulation , no need to specify cut-offs right. am using 8x8x8 box
and if we don't specify barostat it will again be a NVT simulations right.
vacuum simulations can be done only in NVT ??
sorry if am wrong . please clarify this doubt
thanks in advance



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Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

[Tomek Wlodarski]

Hi All,

The problem is that this is only message I got...
I also  get this Warning:
--
WARNING: Open MPI will create a shared memory backing file in a
directory that appears to be mounted on a network filesystem.
Creating the shared memory backup file on a network file system, such
as NFS or Lustre is not recommended -- it may cause excessive network
traffic to your file servers and/or cause shared memory traffic in
Open MPI to be much slower than expected.

You may want to check what the typical temporary directory is on your
node.  Possible sources of the location of this temporary directory
include the $TEMPDIR, $TEMP, and $TMP environment variables.

Note, too, that system administrators can set a list of filesystems
where Open MPI is disallowed from creating temporary files by settings
the MCA parameter "orte_no_session_dir".

  Local host: n344
  Fileame:/tmp/openmpi-sessions-didymos@n344_0
/19430/1/shared_mem_pool.n344

You can set the MCA paramter shmem_mmap_enable_nfs_warning to 0 to
disable this message.
--

but this I got also with gromacs 4.5.5 which is running ok so I think this
is not a problem in my case.

Like Alexey notice the problem is that my nodes have different
architecture.. but this was not a problem with gromacs 4.5.5

My access node:

processor: 0
vendor_id: AuthenticAMD
cpu family: 21
model: 1
model name: AMD Opteron(TM) Processor 6272
stepping: 2
cpu MHz: 2400.003
cache size: 2048 KB
physical id: 0
siblings: 16
core id: 0
cpu cores: 16
apicid: 32
initial apicid: 0
fpu: yes
fpu_exception: yes
cpuid level: 13
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx
 mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc nonstop_tsc extd_apicid
amd_dcm pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 po
pcnt aes xsave avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a
misalignsse 3dnowprefetch osvw ibs xop skinit wdt nodeid_m
sr arat
bogomips: 4199.99
TLB size: 1536 4K pages
clflush size: 64
cache_alignment: 64
address sizes: 48 bits physical, 48 bits virtual
power management: ts ttp tm 100mhzsteps hwpstate [9]

My computational node:

processor: 0
vendor_id: AuthenticAMD
cpu family: 16
model: 2
model name: Quad-Core AMD Opteron(tm) Processor 8354
stepping: 3
cpu MHz: 2200.001
cache size: 512 KB
physical id: 0
siblings: 4
core id: 0
cpu cores: 4
apicid: 0
initial apicid: 0
fpu: yes
fpu_exception: yes
cpuid level: 5
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx
 mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc rep_good
nonstop_tsc extd_apicid pni monitor cx16 popcnt lahf_lm c
mp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw
ibs
bogomips: 4399.99
TLB size: 1024 4K pages
clflush size: 64
cache_alignment: 64
address sizes: 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate

Thanks a lot!

Best!

tomek




On Sun, Feb 17, 2013 at 2:37 PM, Alexey Shvetsov wrote:

> Hi!
>
> В письме от 16 февраля 2013 23:27:45 пользователь Tomek Wlodarski написал:
> > Hi!
> >
> > I have problem in running gromacs 4.6 in PBS queue...
> > I end up with error:
> >
> >
> > [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv
> > failed: Connection reset by peer (104)
> >
> --
> > mpirun noticed that process rank 18 with PID 616 on node n344 exited on
> > signal 4 (Illegal instruction).
>
> Aha. Your mdrun process got SIGILL. This means that your nodes have
> different
> instruction set then head node. So try to use different acceleration level.
> Can you share details about your hw?
>
> >
> --
> > [n370:03036] 3 more processes have sent help message
> > help-opal-shmem-mmap.txt / mmap on nfs
> > [n370:03036] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
> > help / error messages
> > 3 total processes killed (some possibly by mpirun during cleanup)
> >
> > I run the same pbs files with older gromacs 4.5.5 (installed with the
> same
> > openmpi, gcc and fftw) and everything is working..
> >
> > also when I am running gromacs directly on the access node:
> >
> > mpirun -np 32 /home/users/didymos/gromacs/bin/mdrun_mpi -v -deffnm
> > protein-EM-solvated -c protein-EM-solvated.gro
> >
> > it is running OK.
> > Any ideas?
> > Thank you!
> > Best!
> >
> > tomek
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Ins

Re: [gmx-users] Re: vaccum simulation error

[Erik Marklund]

Ponder this: What is the pressure of vacuum?

On Feb 19, 2013, at 12:32 PM, raji wrote:

for vacuum simulation , no need to specify cut-offs right. am using  
8x8x8 box
and if we don't specify barostat it will again be a NVT simulations  
right.

vacuum simulations can be done only in NVT ??
sorry if am wrong . please clarify this doubt
thanks in advance



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Re: [gmx-users] Re: A note while running grompp for nvt equilibration

[Justin Lemkul]

On 2/19/13 1:36 AM, Anu Chandran wrote:

Sir,
Thank you for the reply. As per the suggestion, I tried increasing the
rlist. Note or warning stopped when rlist was increased to 1.8. Also with
this value of rcoulomb, the box size also needs to be increased. I would
like to know whether it is fine to keep rlist 1.8 and also whether there is
any other alternative rather than increasing rlist since increase in rlist
requires an increase in box size.


I would investigate why you have such large charge groups.  For a protein in 
water (which is what you appear to have based on the .mdp file), you should not 
have such large charge groups.  Haphazardly adjusting cutoffs can have a 
negative effect on the simulation.  Increasing rlist may result in poorer 
performance.  Why are you using a switching potential for van der Waals 
interactions?  Exact specifications for OPLS are hard to come by in the 
literature, but most commonly one sees:


rvdw = 1.0
vdwtype = cutoff
rlist = 1.0
rcoulomb = 1.0
coulombtype = PME

-Justin


Thank you,
with regards
Anu

On Fri, Feb 15, 2013 at 5:28 PM, Dr. Vitaly Chaban wrote:


I am tyring to do a simulation of a monomer and an octamer of the same
molecule
using gromacs 4.5.3 with opls force field. Monomer simulations ran with

out

any note or
warning, but when i tried to do nvt equilibration for the octamer, i got

the

following note while running grompp

"NOTE 1 [file nvt.mdp]:
   The sum of the two largest charge group radii (0.779095) is larger than
   rlist (1.40) - rvdw (1.00)"
The mdp file used is as follows:

define  = -DPOSRES
integrator  = md
dt  = 0.002
nsteps  = 5
nstcomm = 10
nstxout = 100
nstvout = 100
nstlog  = 100
nstenergy   = 100
nstlist = 5
ns_type = grid
pbc = xyz
rlist   = 1.4
coulombtype = PME
rcoulomb= 1.4
epsilon_r   = 1
vdwtype = Switch
rvdw_switch = 0.9
rvdw= 1.00
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
Tcoupl  = nose_hoover
tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4
ref_t   = 300  300
nh-chain-length = 1
pcoupl  = no
gen_vel = yes
gen_temp= 300.0
gen_seed= 1984
continuation = no
constraints  = all-bonds
constraint-algorithm = LINCS
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30


Can anybody please help me on how to go about with it?



1) Increase RLIST
2) Re-distribute atoms among charge groups so that to make charge
groups [spatially] smaller.



Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
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Re: [gmx-users] rtp topology file for ligand

[Justin Lemkul]

On 2/19/13 4:23 AM, amna khan wrote:

hi all,

  i generated the .itp file for my ligand using ATB,
and i have generated the protein topology file by using the forcefield 13

my question is i need to generate the *ligand .top and .gro files*

and when i use the command


*pdb2gmx -f  lig.pdb -o igand.gro -i lig.itp -p iig.top

*
*the error arises that
Fatal error:
Residue 'LIG' not found in residue topology database


*
what should i do ?

how to create the rtp file for my ligand ... i have read the tutorail but i
am not getting it what steps* exactly should i do please please help me and
guide me in making the .rtp file for my ligand
*



Chapter 5 of the manual describes .rtp format, but you don't need it.  You 
already have a ligand topology from ATB, so why ask pdb2gmx to do it over again? 
 Remove the ligand from the coordinate file and deal with it separately.  I 
don't know which tutorial you're referring to, but you should at least try to 
follow the protocol I describe here:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

-Justin

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Re: [gmx-users] There was 1 error in input file(s)

[Justin Lemkul]

On 2/19/13 4:29 AM, 라지브간디 wrote:

Dear GMX users,


I have done nvt part and then start to do npt part for my protein but it shows 
error like


Fatal error:
There was 1 error in input file(s)


Please how can avoid this?



Fix the error :)  In seriousness, no one can help you unless you provide 
relevant information.  At minimum, that requires the actual error message (which 
grompp will have printed out earlier in the screen output).  You should also 
consult http://www.gromacs.org/Documentation/Errors, where all of the most 
common errors and their solutions are described.


-Justin

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Re: [gmx-users] error in editconf

[Justin Lemkul]

On 2/19/13 4:53 AM, az kalsom wrote:

hi all,

i generated the ligand topology file by prodrg server and then i generated
the .out file from gaussain software aund used itp adjuster to adjsut the
charges in ligand itp file

but still i am getting the bad box error when i run the editconf command

why is this so what should i do to correct this ?



"Bad box" errors usually mean you don't have box vectors in the coordinate file 
or that the number of atoms specified in the .gro file is incorrect, leading to 
editconf reading a coordinate entry as box vectors.  Without the first 2 lines 
and last line of the .gro file, as well as the output of wc -l on the file, it's 
impossible to say what the real problem is.


-Justin

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Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

[Bogdan Costescu]

On Tue, Feb 19, 2013 at 1:32 PM, Tomek Wlodarski
 wrote:
> The problem is that this is only message I got...

But that's an important error. GROMACS 4.6 depends a lot on the
compiler generated code, as opposed to 4.5 and previous which used
hand-written assembler code. The build procedure detects the
architecture and instructs the compiler to optimize for it. If the
computer on which you build GROMACS 4.6 has a different architecture
from the one on which the executables are run, you get exactly this
error. F.e. if your build computer is has Intel Sandy Bridge
CPUs and the compute nodes have AMD Magny Cours CPUs, the executable
won't run. You have to instruct the build procedure to use the proper
type of acceleration for the compute nodes where the executable will
be run.

> I also  get this Warning:
> --
> WARNING: Open MPI will create a shared memory backing file in a
> directory that appears to be mounted on a network filesystem.

OpenMPI users have found that shared memory performance was lower when
the shared memory backing file was created on a shared file system.
This mechanism is used by default when you run several MPI ranks on
the same computer. There's some documentation on the OpenMPI site on
the implications and how to control this.

> but this I got also with gromacs 4.5.5 which is running ok so I think this
> is not a problem in my case.

... so performance with GROMACS 4.5.5 might have also suffered from this :)

> Like Alexey notice the problem is that my nodes have different
> architecture.. but this was not a problem with gromacs 4.5.5

Indeed, for the reason I mentioned above. Check for example the
presence/absence of "avx" in the "flags" section.

Cheers,
Bogdan
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Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

[Richard Broadbent]

Hi Tomek,

Gromacs 4.6 uses very different accelerated kernels to 4.5.5. These are 
hardware specific and you must therefore select acceleration appropriate 
for your hardware.


your login node will automatically use and select AVX-128-FMA 
acceleration. However, your compute nodes are considerably older and 
they need sse2 acceleration instead.

adding:

-DGMX_CPU_ACCELERATION=SSE2

to your cmake line should fix this.

The Open MPI warning is an issue with how your jobs are setup to run on 
your system. I would suggest discussing it with your system 
administrator as that might cause a significant slow down in your 
simulation as well as for other cluster users.


Richard



On 19/02/13 12:32, Tomek Wlodarski wrote:

Hi All,

The problem is that this is only message I got...
I also  get this Warning:
--
WARNING: Open MPI will create a shared memory backing file in a
directory that appears to be mounted on a network filesystem.
Creating the shared memory backup file on a network file system, such
as NFS or Lustre is not recommended -- it may cause excessive network
traffic to your file servers and/or cause shared memory traffic in
Open MPI to be much slower than expected.

You may want to check what the typical temporary directory is on your
node.  Possible sources of the location of this temporary directory
include the $TEMPDIR, $TEMP, and $TMP environment variables.

Note, too, that system administrators can set a list of filesystems
where Open MPI is disallowed from creating temporary files by settings
the MCA parameter "orte_no_session_dir".

   Local host: n344
   Fileame:/tmp/openmpi-sessions-didymos@n344_0
/19430/1/shared_mem_pool.n344

You can set the MCA paramter shmem_mmap_enable_nfs_warning to 0 to
disable this message.
--

but this I got also with gromacs 4.5.5 which is running ok so I think this
is not a problem in my case.

Like Alexey notice the problem is that my nodes have different
architecture.. but this was not a problem with gromacs 4.5.5

My access node:

processor: 0
vendor_id: AuthenticAMD
cpu family: 21
model: 1
model name: AMD Opteron(TM) Processor 6272
stepping: 2
cpu MHz: 2400.003
cache size: 2048 KB
physical id: 0
siblings: 16
core id: 0
cpu cores: 16
apicid: 32
initial apicid: 0
fpu: yes
fpu_exception: yes
cpuid level: 13
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx
  mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc nonstop_tsc extd_apicid
amd_dcm pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 po
pcnt aes xsave avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a
misalignsse 3dnowprefetch osvw ibs xop skinit wdt nodeid_m
sr arat
bogomips: 4199.99
TLB size: 1536 4K pages
clflush size: 64
cache_alignment: 64
address sizes: 48 bits physical, 48 bits virtual
power management: ts ttp tm 100mhzsteps hwpstate [9]

My computational node:

processor: 0
vendor_id: AuthenticAMD
cpu family: 16
model: 2
model name: Quad-Core AMD Opteron(tm) Processor 8354
stepping: 3
cpu MHz: 2200.001
cache size: 512 KB
physical id: 0
siblings: 4
core id: 0
cpu cores: 4
apicid: 0
initial apicid: 0
fpu: yes
fpu_exception: yes
cpuid level: 5
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx
  mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc rep_good
nonstop_tsc extd_apicid pni monitor cx16 popcnt lahf_lm c
mp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw
ibs
bogomips: 4399.99
TLB size: 1024 4K pages
clflush size: 64
cache_alignment: 64
address sizes: 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate

Thanks a lot!

Best!

tomek




On Sun, Feb 17, 2013 at 2:37 PM, Alexey Shvetsov wrote:


Hi!

В письме от 16 февраля 2013 23:27:45 пользователь Tomek Wlodarski написал:

Hi!

I have problem in running gromacs 4.6 in PBS queue...
I end up with error:


[n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv
failed: Connection reset by peer (104)


--

mpirun noticed that process rank 18 with PID 616 on node n344 exited on
signal 4 (Illegal instruction).


Aha. Your mdrun process got SIGILL. This means that your nodes have
different
instruction set then head node. So try to use different acceleration level.
Can you share details about your hw?




--

[n370:03036] 3 more processes have sent help message
help-opal-shmem-mmap.txt / mmap on 

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

[Mark Abraham]

but this I got also with gromacs 4.5.5 which is running ok so I think this

> is not a problem in my case.
>
> Like Alexey notice the problem is that my nodes have different
> architecture.. but this was not a problem with gromacs 4.5.5
>

Yes, that is expected. Probably both machines support SSE2, which is all
the acceleration that was available in 4.5.x, so there was no issue
then. It's also why I asked to see the head of the .log file, because that
will show what the runtime machine can do - search for "Acceleration most
likely". In 4.6, CMake detects what is available on the build machine, and
if you don't instruct it otherwise, compiles for the build machine. You can
look at the head of the .log file for , and then do a build where you set
GMX_CPU_ACCELERATION accordingly (either in ccmake, or via -D on the
command line).

Mark
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[gmx-users] terminal phosphate residue for dna simulations

[Vedat Durmaz]

hi guys,

does anyone know about a way to simulate mono- or polynucleotides along 
with a 3' or 5' bound monophosphate using an amber force field like 
ffamber99sb?


i couldn't find any residue definition for a terminal phosphate group 
such as " P3' " or " P5' " (exemplarily). do they indeed not exist or am 
i just not able to search them?


thanks in advance & take care
vedat


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Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

[Tomek Wlodarski]

Hi,

Thanks All for help.
Now is working!
Best!

tomek



On Tue, Feb 19, 2013 at 2:38 PM, Mark Abraham wrote:

> but this I got also with gromacs 4.5.5 which is running ok so I think this
>
> > is not a problem in my case.
> >
> > Like Alexey notice the problem is that my nodes have different
> > architecture.. but this was not a problem with gromacs 4.5.5
> >
>
> Yes, that is expected. Probably both machines support SSE2, which is all
> the acceleration that was available in 4.5.x, so there was no issue
> then. It's also why I asked to see the head of the .log file, because that
> will show what the runtime machine can do - search for "Acceleration most
> likely". In 4.6, CMake detects what is available on the build machine, and
> if you don't instruct it otherwise, compiles for the build machine. You can
> look at the head of the .log file for , and then do a build where you set
> GMX_CPU_ACCELERATION accordingly (either in ccmake, or via -D on the
> command line).
>
> Mark
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Re: [gmx-users] terminal phosphate residue for dna simulations

[Paulo Netz]

Hi Vedat

First of all, the coordinates input file (for instance, pdb) must have
terminal
nucleotides with "free", dangling phosphate groups. In most of the cases,
such terminal phosphates are absent. If the structure indeed has these
phosphates, it is possible to simulate a mono-, oligo- or polynucleotide
displaying these dangling phosphates with AMBER force field. You only
have to consider that the nucleotide definition of AMBER distinguishes
between the terminal nucleotides (normally without phosphate,
named for instance as DA3, DA5, DT3, DT5 etc.) and the regular nucleotides
(DA, DT, DC, DG). You just have to consider your terminal nucleotides
as regular ones (i.e. named as DA instead of DA3 or DA5 and so on).
More details you can find in my paper:

doi: *10.1021*/*jp1035663*
*
*
Best regards

Paulo Netz


On Tue, Feb 19, 2013 at 10:35 AM, Vedat Durmaz  wrote:

> hi guys,
>
> does anyone know about a way to simulate mono- or polynucleotides along
> with a 3' or 5' bound monophosphate using an amber force field like
> ffamber99sb?
>
> i couldn't find any residue definition for a terminal phosphate group such
> as " P3' " or " P5' " (exemplarily). do they indeed not exist or am i just
> not able to search them?
>
> thanks in advance & take care
> vedat
>
>
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[gmx-users] comm-grps

[fciocco]

Hi

I want to study the interaction between a peptide and a lipid bilayer, with
the peptide initialy outside de bilayer.  Is correct to choose only
"bilayer" and "SOL_ions" as comm-groups ? because grompp complain about that
with a warning: some atoms are not part of any center of mass motion removal
group. This may lead to artifacts.

any help would be very appreciated.

best regards, Facundo



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[gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

[jneeraj]

Hello,

I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs
ver 4.5.5 with charmm27 force-field. 
Though charmm27 force-field (top_all27_prot_lipid.inp, also see 
http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm
  ) has
the force-field parameters for residue ETAM, charmm27.ff of gromacs does not
define ETAM residue. Is there any quick way of importing ETAM residue from
top_all27_prot_lipid.inp to charmm27.ff ?

Thank you,
Neeraj



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Re: [gmx-users] cmaptypes format

[Per Larsson]

Hi Francesco

That number corresponds to a type for each cmap-entry. The idea (iirc, it was 
some time ago) was that it could be useful to be able to have multiple 
cmap-types (other grid values, different grid spacing etc) for the same 
cmap-dihedral (much like different torsions etc...), but based on a quick look 
in the code, the support for that is very limited. It should probably not be 
touched right now.

Cheers
/Per


19 feb 2013 kl. 15:43 skrev francesco oteri:

> Dear gromacs users,
> I am trying to figure out the meaning of the cmaptypes section in file
> section.
> As far as I understood, taking the following entry as example:
> 
> C NH1 CT1 C NH1 1 24 24\
> 
> C NH1 CT1 C   = phi
> H1 CT1 C NH1 = psi
> 
> 24*24 = dimension of the grid
> 
> My question is: what does the 1 mean?
> 
> Best,
> Francesco
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Re: [gmx-users] cmaptypes format

[francesco oteri]

Thank you so much


2013/2/19 Per Larsson 

> Hi Francesco
>
> That number corresponds to a type for each cmap-entry. The idea (iirc, it
> was some time ago) was that it could be useful to be able to have multiple
> cmap-types (other grid values, different grid spacing etc) for the same
> cmap-dihedral (much like different torsions etc...), but based on a quick
> look in the code, the support for that is very limited. It should probably
> not be touched right now.
>
> Cheers
> /Per
>
>
> 19 feb 2013 kl. 15:43 skrev francesco oteri:
>
> > Dear gromacs users,
> > I am trying to figure out the meaning of the cmaptypes section in file
> > section.
> > As far as I understood, taking the following entry as example:
> >
> > C NH1 CT1 C NH1 1 24 24\
> >
> > C NH1 CT1 C   = phi
> > H1 CT1 C NH1 = psi
> >
> > 24*24 = dimension of the grid
> >
> > My question is: what does the 1 mean?
> >
> > Best,
> > Francesco
> > --
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-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] NVT and NPT Equalibration

[Justin Lemkul]

On 2/19/13 10:07 AM, Sainitin Donakonda wrote:

Hi all,

I want simulate my protein ligand complex for 20 nanoseconds..(final
production run)

So i set up NVT and NPT equlibrations for 200 ps each..

Can anyone tell me is this correct ? to setup 200 ps prior to 20 ns MD
production?



There is no universal answer to this question.  Equilibration is done when it is 
done.  Measure the observables of interest and if they have converged, then the 
equilibration protocol was sufficient.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

[Justin Lemkul]

On 2/19/13 9:41 AM, jneeraj wrote:

Hello,

I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs
ver 4.5.5 with charmm27 force-field.
Though charmm27 force-field (top_all27_prot_lipid.inp, also see
http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm
  ) has
the force-field parameters for residue ETAM, charmm27.ff of gromacs does not
define ETAM residue. Is there any quick way of importing ETAM residue from
top_all27_prot_lipid.inp to charmm27.ff ?



It's a simple molecule, so writing a topology by hand should be rather trivial. 
 Consult Chapter 5 of the manual for specifics.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] comm-grps

[Justin Lemkul]

On 2/19/13 9:25 AM, fciocco wrote:

Hi

I want to study the interaction between a peptide and a lipid bilayer, with
the peptide initialy outside de bilayer.  Is correct to choose only
"bilayer" and "SOL_ions" as comm-groups ? because grompp complain about that
with a warning: some atoms are not part of any center of mass motion removal
group. This may lead to artifacts.



That setup leaves the protein unaccounted for, hence the warning from grompp. 
This is a tricky system to deal with, because the associations between molecules 
will change over time; it's not as easy as a pure membrane (where water and 
lipids might be in separate groups) or a protein in water (where the whole 
system is the only sensible group).  In my mind, the only appropriate setting 
here is "comm-grps = System."


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] rtp topology file for ligand

[amna khan]

yes i am following this tutorial too

this is my topology file for the ligand i made by atb

*http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045

*
*from here i got the .itp file and optimzed ligand.pdb file but what about
the .gro file and .top file
*
*i ran that command to make the .gro and .top file of ligand 
*
*this is as follows
*

pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p
my_ligand.top.

this generated the fetal error

Fatal error:
Residue 'LIG' not found in residue topology database

SO WHAT SHOULD I DO ABOUT THIS PROBLEM


On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul  wrote:

>
>
> On 2/19/13 4:23 AM, amna khan wrote:
>
>> hi all,
>>
>>   i generated the .itp file for my ligand using ATB,
>> and i have generated the protein topology file by using the forcefield 13
>>
>> my question is i need to generate the *ligand .top and .gro files*
>>
>>
>> and when i use the command
>>
>>
>> *pdb2gmx -f  lig.pdb -o igand.gro -i lig.itp -p iig.top
>>
>> *
>> *the error arises that
>>
>> Fatal error:
>> Residue 'LIG' not found in residue topology database
>>
>>
>> *
>> what should i do ?
>>
>> how to create the rtp file for my ligand ... i have read the tutorail but
>> i
>> am not getting it what steps* exactly should i do please please help me
>> and
>>
>> guide me in making the .rtp file for my ligand
>> *
>>
>>
> Chapter 5 of the manual describes .rtp format, but you don't need it.  You
> already have a ligand topology from ATB, so why ask pdb2gmx to do it over
> again?  Remove the ligand from the coordinate file and deal with it
> separately.  I don't know which tutorial you're referring to, but you
> should at least try to follow the protocol I describe here:
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
> gmx-tutorials/complex/index.**html
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] Dihedral angel

[라지브간디]

I want to calculate the dihedral angel of side chain of Arginine. could you 
tell how it can be done? how do i create ndx for Arg and look at the dihedral 
angel in sinumation time point ?

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Re: [gmx-users] rtp topology file for ligand

[Justin Lemkul]

On 2/19/13 10:53 AM, amna khan wrote:

yes i am following this tutorial too

this is my topology file for the ligand i made by atb

*http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045

*
*from here i got the .itp file and optimzed ligand.pdb file but what about
the .gro file and .top file
*
*i ran that command to make the .gro and .top file of ligand 
*
*this is as follows
*

pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p
my_ligand.top.

this generated the fetal error

Fatal error:
Residue 'LIG' not found in residue topology database

SO WHAT SHOULD I DO ABOUT THIS PROBLEM



Follow the tutorial more closely.  pdb2gmx will not deal with your ligand, so 
remove its coordinates from the protein-ligand complex and only run the protein 
through pdb2gmx.  You do not need pdb2gmx to make a topology for the ligand - 
you already have the topology in .itp format from ATB.  If you need the ligand 
coordinates in .gro format, simply transform from .pdb to .gro using edticonf. 
The job of pdb2gmx is to produce a topology, an output coordinate file is a side 
effect.


You do not need a separate .top file for the ligand.  A .top file is a system 
topology, encompassing all elements of the system and thus there can only be 
one.  Other molecules (like your ligand) are #included in the system .top file 
using .itp format.


-Justin



On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul  wrote:




On 2/19/13 4:23 AM, amna khan wrote:


hi all,

   i generated the .itp file for my ligand using ATB,
and i have generated the protein topology file by using the forcefield 13

my question is i need to generate the *ligand .top and .gro files*


and when i use the command


*pdb2gmx -f  lig.pdb -o igand.gro -i lig.itp -p iig.top

*
*the error arises that

Fatal error:
Residue 'LIG' not found in residue topology database


*
what should i do ?

how to create the rtp file for my ligand ... i have read the tutorail but
i
am not getting it what steps* exactly should i do please please help me
and

guide me in making the .rtp file for my ligand
*



Chapter 5 of the manual describes .rtp format, but you don't need it.  You
already have a ligand topology from ATB, so why ask pdb2gmx to do it over
again?  Remove the ligand from the coordinate file and deal with it
separately.  I don't know which tutorial you're referring to, but you
should at least try to follow the protocol I describe here:

http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
gmx-tutorials/complex/index.**html

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==
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 posting!
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Dihedral angel

[Justin Lemkul]

On 2/19/13 10:52 AM, 라지브간디 wrote:

I want to calculate the dihedral angel of side chain of Arginine. could you 
tell how it can be done? how do i create ndx for Arg and look at the dihedral 
angel in sinumation time point ?



g_angle will measure the dihedral.  Refer to g_angle -h for available options. 
The index file itself is trivial to create manually with a text editor.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] rtp topology file for ligand

[amna khan]

i generated the ligand.gro by using the command

*editconf -g my_otp_ligand.pdb -o ligand.gro*
*
*
*WARNING: all CONECT records are ignored*
*Read 38 atoms*
*No velocities found*

it printed this and after this i did as mention in tutorial

it generated the bad box error  and the wc -l comand result is as follows

*and wc -l conf.gro
*
*2237 conf.gro*
*
*
*
*
*the first three lines *
*
2196
  705SER  N1  -3.373  -1.131   1.295
  705SER H12  -3.442  -1.166   1.232
  705SER H23  -3.339  -1.043   1.261
  705SER H34  -3.298  -1.196   1.303


and last three lines are
0_NFPHO   36  -0.376  -0.128   0.141
0_NFP   C26   37  -0.328   0.137  -0.081
0_NFP   C27   38  -0.293   0.373  -0.168
   9.21266   2.62220   3.05500


what is woring with ligand to gro converion ?

why this bad box error arose ?


regards
amna khan
*







On Tue, Feb 19, 2013 at 8:58 PM, Justin Lemkul  wrote:

>
>
> On 2/19/13 10:53 AM, amna khan wrote:
>
>> yes i am following this tutorial too
>>
>> this is my topology file for the ligand i made by atb
>>
>> *http://compbio.biosci.uq.edu.**au/atb/download.py?molid=7045
>>
>> *
>> *from here i got the .itp file and optimzed ligand.pdb file but what about
>>
>> the .gro file and .top file
>> *
>> *i ran that command to make the .gro and .top file of ligand 
>> *
>> *this is as follows
>> *
>>
>>
>> pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p
>> my_ligand.top.
>>
>> this generated the fetal error
>>
>> Fatal error:
>> Residue 'LIG' not found in residue topology database
>>
>> SO WHAT SHOULD I DO ABOUT THIS PROBLEM
>>
>>
> Follow the tutorial more closely.  pdb2gmx will not deal with your ligand,
> so remove its coordinates from the protein-ligand complex and only run the
> protein through pdb2gmx.  You do not need pdb2gmx to make a topology for
> the ligand - you already have the topology in .itp format from ATB.  If you
> need the ligand coordinates in .gro format, simply transform from .pdb to
> .gro using edticonf. The job of pdb2gmx is to produce a topology, an output
> coordinate file is a side effect.
>
> You do not need a separate .top file for the ligand.  A .top file is a
> system topology, encompassing all elements of the system and thus there can
> only be one.  Other molecules (like your ligand) are #included in the
> system .top file using .itp format.
>
> -Justin
>
>
>> On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/19/13 4:23 AM, amna khan wrote:
>>>
>>>  hi all,

i generated the .itp file for my ligand using ATB,
 and i have generated the protein topology file by using the forcefield
 13

 my question is i need to generate the *ligand .top and .gro files*


 and when i use the command


 *pdb2gmx -f  lig.pdb -o igand.gro -i lig.itp -p iig.top

 *
 *the error arises that

 Fatal error:
 Residue 'LIG' not found in residue topology database


 *
 what should i do ?

 how to create the rtp file for my ligand ... i have read the tutorail
 but
 i
 am not getting it what steps* exactly should i do please please help me
 and

 guide me in making the .rtp file for my ligand
 *


  Chapter 5 of the manual describes .rtp format, but you don't need it.
>>>  You
>>> already have a ligand topology from ATB, so why ask pdb2gmx to do it over
>>> again?  Remove the ligand from the coordinate file and deal with it
>>> separately.  I don't know which tutorial you're referring to, but you
>>> should at least try to follow the protocol I describe here:
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>> gmx-tutorials/complex/index.html>> biochem.vt.edu/Pages/Personal/**justin/gmx-tutorials/complex/**
>>> index.html
>>> >
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
>>> posting!
>>>
>>> * Please d

Re: [gmx-users] rtp topology file for ligand

[Justin Lemkul]

On 2/19/13 12:53 PM, amna khan wrote:

i generated the ligand.gro by using the command

*editconf -g my_otp_ligand.pdb -o ligand.gro*
*
*
*WARNING: all CONECT records are ignored*
*Read 38 atoms*
*No velocities found*

it printed this and after this i did as mention in tutorial

it generated the bad box error  and the wc -l comand result is as follows

*and wc -l conf.gro
*
*2237 conf.gro*
*
*
*
*
*the first three lines *
*
2196
   705SER  N1  -3.373  -1.131   1.295
   705SER H12  -3.442  -1.166   1.232
   705SER H23  -3.339  -1.043   1.261
   705SER H34  -3.298  -1.196   1.303


and last three lines are
 0_NFPHO   36  -0.376  -0.128   0.141
 0_NFP   C26   37  -0.328   0.137  -0.081
 0_NFP   C27   38  -0.293   0.373  -0.168
9.21266   2.62220   3.05500


what is woring with ligand to gro converion ?

why this bad box error arose ?



The number of atoms is wrong.  The wc -l command says there are 2237 lines in 
the .gro file, so subtracting three (for the title, number of atoms line, and 
box vectors at the end) says you have 2234 atoms in the file.  The second line 
of the .gro file needs to be changed to read 2234 instead of 2196.  The bad box 
error arises because editconf stops reading atoms at atom 2196 and expects the 
next line to be vectors, but instead finds more atoms.  Again, all of this is 
described in the tutorial in explicit detail; please pay very close attention to 
its instructions.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] trjconv woes (broken molecules)

[Ignacio Fernández Galván]

Hi all,

I have a simulation with a frozen molecule which stays around the origin, and a 
number of solvent molecules with pbc. Due to the way the simulation cell is 
defined, with a corner at the origin, by default my frozen molecule appears 
broken, a piece on every corner of the box, and I want it whole (and if 
possible centered).

In a simple world, I'd use trjconv with -pbc res (or mol) and -center, but of 
course, that doesn't work when initially the molecule is broken, as its center 
of mass is in a meaningless position. I can use -pbc atom, but then the solvent 
molecules get broken.

So I assume I have to use a multi-step conversion, and I have to first get a 
whole molecule. But I tried -pbc whole and -pbc cluster and they don't make any 
difference.

I can't find anything that works reliably, can anybody help me?

Thank you
Ignacio
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[gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

[Bryan Roessler]

Hello,

I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The
ATP residue is stored in a toppar stream file in CHARMM, thus it is not
included in the download on the user-submission page for FFs. It also
appears that it is not available in the AMBER forcefields.

It is however, present in the GROMOS FF supplied with GROMACS and also
available on the user-submission website. However, I have reservations
about using a united-atom FF in conjunction with CHARMM (which is how the
rest of my system is parameterized). I've also taken a PDB of ATP and
parameterized it with SWISS-PARAM, however the user-submitted
'CHARMM2GROMACS' scripts are not successfully parsing the
topology/parameter files and not generating valid GROMACS output.

If anyone has a CHARMM FF for ATP that is in >GROMACS4.5.4 format, I would
be much obliged. If it is not available, I could use some help in
understanding how to convert toppar stream entries from CHARMM into the
GROMACS format.


Thank you,

Bryan Roessler
The University of Alabama-Birmingham
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Re: [gmx-users] trjconv woes (broken molecules)

[Justin Lemkul]

On 2/19/13 1:28 PM, Ignacio Fernández Galván wrote:

Hi all,

I have a simulation with a frozen molecule which stays around the origin, and a 
number of solvent molecules with pbc. Due to the way the simulation cell is 
defined, with a corner at the origin, by default my frozen molecule appears 
broken, a piece on every corner of the box, and I want it whole (and if 
possible centered).

In a simple world, I'd use trjconv with -pbc res (or mol) and -center, but of 
course, that doesn't work when initially the molecule is broken, as its center 
of mass is in a meaningless position. I can use -pbc atom, but then the solvent 
molecules get broken.

So I assume I have to use a multi-step conversion, and I have to first get a 
whole molecule. But I tried -pbc whole and -pbc cluster and they don't make any 
difference.



First use:

trjconv -trans x y z -pbc mol

This will allow you to reposition the elements of your system such that you have 
an intact structure at the origin.  Then use the structure created as your new 
reference structure for further trjconv iterations (removing jumps, making 
molecules whole, etc).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

[Justin Lemkul]

On 2/19/13 1:29 PM, Bryan Roessler wrote:

Hello,

I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The
ATP residue is stored in a toppar stream file in CHARMM, thus it is not
included in the download on the user-submission page for FFs. It also
appears that it is not available in the AMBER forcefields.

It is however, present in the GROMOS FF supplied with GROMACS and also
available on the user-submission website. However, I have reservations
about using a united-atom FF in conjunction with CHARMM (which is how the
rest of my system is parameterized). I've also taken a PDB of ATP and


Mixing and matching is always a terrible idea, especially when the force fields 
in question share basically no attributes in common.



parameterized it with SWISS-PARAM, however the user-submitted
'CHARMM2GROMACS' scripts are not successfully parsing the
topology/parameter files and not generating valid GROMACS output.

If anyone has a CHARMM FF for ATP that is in >GROMACS4.5.4 format, I would
be much obliged. If it is not available, I could use some help in
understanding how to convert toppar stream entries from CHARMM into the
GROMACS format.



Googling turns up a few results, at least one of which may be of particular 
interest:


http://gromacs.5086.n6.nabble.com/Nucleotides-for-charmm-port-td934.html

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Diagonalizing matrix (g_covar)

[SeokYun123]

I'm trying to obtain eigenvalues as well as eigenvectors from the matrix by
diagonalizing it.

I don't know, is there a way to simplify the problem? 

How about scalapack or mkl?

I heard that those two pose same problems as well.

Thank you.



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Re: [gmx-users] NO velocities for ligand

[Justin Lemkul]

On 2/19/13 2:39 PM, amna khan wrote:

hello sir,

i want to ask  you i have GNERATED the ligand topolagy file by ATB

and converting the optimized pdb to gro
by editconf, it doesnot generated the volecities for ligand ,

why is this ?



Because editconf has no business generating velocities.  Velocities are 
irrelevant until using grompp.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] Problem with g_rdf

[Thomas Schlesier]

Dear all,
I have a question regarding g_rdf.
My system consits of 10 disacchardids (in the following A-B, with 
A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine 
the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular 
for A-B


A-A and B-B is no problem.
But for A-B g_rdf determines the intermolecular contribution (which i 
want) AND the intramolekular contribution (which i wanted to be excluded).


Any (nice) ideas to solve this problem for GMX 4.0.7?

Long way would be to calculate each intermolecular contribution 
individual and average over all. Would require some scripting :( so any 
better solutions are welcome.


Greetings
Thomas
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Re: [gmx-users] Problem with g_rdf

[Justin Lemkul]

On 2/19/13 3:10 PM, Thomas Schlesier wrote:

Dear all,
I have a question regarding g_rdf.
My system consits of 10 disacchardids (in the following A-B, with
A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF
(with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B

A-A and B-B is no problem.
But for A-B g_rdf determines the intermolecular contribution (which i want) AND
the intramolekular contribution (which i wanted to be excluded).

Any (nice) ideas to solve this problem for GMX 4.0.7?

Long way would be to calculate each intermolecular contribution individual and
average over all. Would require some scripting :( so any better solutions are
welcome.



Create a topology with a value of nrexcl sufficient to exclude all 
intramolecular interactions and create a .tpr file from it.  Use that as input 
to g_rdf.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Is it possible to use a force filed for Au?

[Justin Lemkul]

On 2/19/13 4:57 PM, Ali Alizadeh wrote:

Dear All users

There are  a wall(a gold crystal with 111 orientation) and a bulk of
fluid(alkane) in my simulation box,

My problem is, Is it possible to use a force filed for Au? Beside, Can
I use two force field at the same time?



You need a self-consistent force field that adequately describes all of the 
elements of your system.  Mixing and matching, even if syntactically possible 
through topology manipulation, leads to junk that no one should believe.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Problem with g_rdf

[Thomas Schlesier]

On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> Dear all,
> I have a question regarding g_rdf.
> My system consits of 10 disacchardids (in the following A-B, with
> A-ring/monosaccharid and B-ring/monosaccharid) and i want to 
determine the RDF

> (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B
>
> A-A and B-B is no problem.
> But for A-B g_rdf determines the intermolecular contribution (which i 
want) AND

> the intramolekular contribution (which i wanted to be excluded).
>
> Any (nice) ideas to solve this problem for GMX 4.0.7?
>
> Long way would be to calculate each intermolecular contribution 
individual and
> average over all. Would require some scripting :( so any better 
solutions are

> welcome.
>

Create a topology with a value of nrexcl sufficient to exclude all
intramolecular interactions and create a .tpr file from it.  Use that as 
input

to g_rdf.

-Justin

-


Thanks for the suggestion. But it doesn't really fix the problem (or i 
don't get it).
Ok what i have done (as an example only 3 molecules, A1 are all atoms of 
ring A of molecule 1, other stuff analogous)


Index group:
[ A ]
A1  A2  A3
[ B ]
B1  B2  B3
[ both ]
A1  B1  A2  B2  A3  B3

RDF(A-A): chose two times group A
RDF(B-B): chose two times group B
RDF(A-B): ?

If i chose group A and B i get the same result with 'nrexcel 3 or 10', 
i.e. mixing of intra- and intermolecluar A-B distances.
If i chose 'both' two-times, i get the impression the the result is the 
RDF between the whole disaccharides, i.e. A1 and B1 are recognised as 
one molecule (AB)1 and i get the RDF between:

(AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3


I tested this also with an index-file with only 1 molecule.
RDF(A-B) gives the intramolecular RDF
RDF(both) is zero, because the is only one molecule, center of mass 
distance must be zero.

This also doesn't depend on using 'nrexcel 3 or 10'


Did i made a mistake? Or any further ideas?

Greetings
Thomas

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[gmx-users] Re: gmx-users Digest, Vol 106, Issue 101

[Ali Alizadeh]

Dear Justin

Thank you for your reply,

>
>
> On 2/19/13 4:57 PM, Ali Alizadeh wrote:
>> Dear All users
>>
>> There are  a wall(a gold crystal with 111 orientation) and a bulk of
>> fluid(alkane) in my simulation box,
>>
>> My problem is, Is it possible to use a force filed for Au? Beside, Can
>> I use two force field at the same time?
>>
>
> You need a self-consistent force field that adequately describes all of the
> elements of your system.  Mixing and matching, even if syntactically possible
> through topology manipulation, leads to junk that no one should believe.

Why?

 In your opinion, Is there a force field for Au in gromacs? Can I
simulate this system by gromacs?

>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



-- 
Sincerely

Ali Alizadeh
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Re: [gmx-users] Problem with g_rdf

[Justin Lemkul]

On 2/19/13 5:04 PM, Thomas Schlesier wrote:

On 2/19/13 3:10 PM, Thomas Schlesier wrote:
 > Dear all,
 > I have a question regarding g_rdf.
 > My system consits of 10 disacchardids (in the following A-B, with
 > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the 
RDF
 > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B
 >
 > A-A and B-B is no problem.
 > But for A-B g_rdf determines the intermolecular contribution (which i want) 
AND
 > the intramolekular contribution (which i wanted to be excluded).
 >
 > Any (nice) ideas to solve this problem for GMX 4.0.7?
 >
 > Long way would be to calculate each intermolecular contribution individual 
and
 > average over all. Would require some scripting :( so any better solutions are
 > welcome.
 >

Create a topology with a value of nrexcl sufficient to exclude all
intramolecular interactions and create a .tpr file from it.  Use that as input
to g_rdf.

-Justin

-



Thanks for the suggestion. But it doesn't really fix the problem (or i don't get
it).
Ok what i have done (as an example only 3 molecules, A1 are all atoms of ring A
of molecule 1, other stuff analogous)

Index group:
[ A ]
A1  A2  A3
[ B ]
B1  B2  B3
[ both ]
A1  B1  A2  B2  A3  B3

RDF(A-A): chose two times group A
RDF(B-B): chose two times group B
RDF(A-B): ?

If i chose group A and B i get the same result with 'nrexcel 3 or 10', i.e.
mixing of intra- and intermolecluar A-B distances.
If i chose 'both' two-times, i get the impression the the result is the RDF
between the whole disaccharides, i.e. A1 and B1 are recognised as one molecule
(AB)1 and i get the RDF between:
(AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3


I tested this also with an index-file with only 1 molecule.
RDF(A-B) gives the intramolecular RDF
RDF(both) is zero, because the is only one molecule, center of mass distance
must be zero.
This also doesn't depend on using 'nrexcel 3 or 10'


Did i made a mistake? Or any further ideas?



No, I missed a piece of information in your original post.  The nrexcl approach 
only works with -rdf atom.  I would suspect that if you want to use -rdf 
mol_com, you will have to have individual groups for which you want the RDF 
around the central group.  You can analyze all the B groups around each A (and 
vice versa, if you need to) using the -ng flag.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Is it possible to use a force filed for Au?

[Justin Lemkul]

On 2/19/13 5:07 PM, Ali Alizadeh wrote:

Dear Justin

Thank you for your reply,




On 2/19/13 4:57 PM, Ali Alizadeh wrote:

Dear All users

There are  a wall(a gold crystal with 111 orientation) and a bulk of
fluid(alkane) in my simulation box,

My problem is, Is it possible to use a force filed for Au? Beside, Can
I use two force field at the same time?



You need a self-consistent force field that adequately describes all of the
elements of your system.  Mixing and matching, even if syntactically possible
through topology manipulation, leads to junk that no one should believe.


Why?



Force fields have to be derived in a self-consistent manner.  You can't just 
patch together some parameter set for one component of the system and some other 
parameter set for some other component.  Self-consistency is the underlying 
requirement for a sensible simulation.



  In your opinion, Is there a force field for Au in gromacs? Can I
simulate this system by gromacs?



Of course.  Refer to the mailing list archive; simulations involving gold have 
been discussed numerous times.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Problem with g_rdf

[Hector Manuel Manzanilla Granados]

Excuseme dear Dr. Tomas, forgiveme the boldness,
I'm new with this, and I dont know who to address
when I have a problem. My name is Hector, and  I'm
tryng to install the gromacs software in my computer;
I follewed all the steps in the online manual, however
when I compile Gromacs with the instruction: ngmx, I receiveç
the following sentence:


:-)  G  R  O  M  A  C  S  (-:

   Glycine aRginine prOline Methionine Alanine Cystine Serine

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and 
others.
   Copyright (c) 1991-2000, University of Groningen, The 
Netherlands.

 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it 
and/or

  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 
2

 of the License, or (at your option) any later version.

 :-)  ngmx  (-:

Option Filename  Type Description

  -f   traj.xtc  InputTrajectory: xtc trr trj gro g96 pdb 
cpt

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -n  index.ndx  Input, Opt.  Index file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time 
(ps)



---
Program ngmx, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737

Can not open file:
topol.tpr
---

"It's Calling Me to Break my Bonds, Again..." (Van der Graaf)


I don't understand what to do with this, may be you can get me a hint,

thank you very much and excuse me.

Best regards.








On Tue, 19 Feb 2013 23:04:48 +0100
 Thomas Schlesier  wrote:

On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> Dear all,
> I have a question regarding g_rdf.
> My system consits of 10 disacchardids (in the following A-B, with
> A-ring/monosaccharid and B-ring/monosaccharid) and i want to 
determine the RDF
> (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for 
A-B

>
> A-A and B-B is no problem.
> But for A-B g_rdf determines the intermolecular contribution 
(which i want) AND

> the intramolekular contribution (which i wanted to be excluded).
>
> Any (nice) ideas to solve this problem for GMX 4.0.7?
>
> Long way would be to calculate each intermolecular contribution 
individual and
> average over all. Would require some scripting :( so any better 
solutions are

> welcome.
>

Create a topology with a value of nrexcl sufficient to exclude all
intramolecular interactions and create a .tpr file from it.  Use 
that as input

to g_rdf.

-Justin

-


Thanks for the suggestion. But it doesn't really fix the problem (or 
i don't get it).
Ok what i have done (as an example only 3 molecules, A1 are all 
atoms of ring A of molecule 1, other stuff analogous)


Index group:
[ A ]
A1  A2  A3
[ B ]
B1  B2  B3
[ both ]
A1  B1  A2  B2  A3  B3

RDF(A-A): chose two times group A
RDF(B-B): chose two times group B
RDF(A-B): ?

If i chose group A and B i get the same result with 'nrexcel 3 or 
10', i.e. mixing of intra- and intermolecluar A-B distances.
If i chose 'both' two-times, i get the impression the the result is 
the RDF between the whole disaccharides, i.e. A1 and B1 are 
recognised as one molecule (AB)1 and i get the RDF between:

(AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3


I tested this also with an index-file with only 1 molecule.
RDF(A-B) gives the intramolecular RDF
RDF(both) is zero, because the is only one molecule, center of mass 
distance must be zero.

This also doesn't depend on using 'nrexcel 3 or 10'


Did i made a mistake? Or any further ideas?

Greetings
Thomas

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