date:20121207

Re: [gmx-users] area per lipid

2012-12-07 Thread Shima Arasteh

Hi again,

I edited my md.mdp files. I'm wondering if my nvt.mdp and npt.mdp in charmm36 
ff also need such a edition? 
Also I'd like to know if these mdp file are applicable in any simulation done 
with charmm36?



Sincerely,
Shima


From: Justin Lemkul 
To: Shima Arasteh  
Sent: Friday, November 9, 2012 3:49 PM
Subject: Re: [gmx-users] area per lipid



On 11/9/12 1:46 AM, Shima Arasteh wrote:
>
>
> I pick the snapshots every 10ns, because I don't know how much time this 
> system needs to be simulated to reach to the proper APL.
>

What I'm saying is there are far better ways to assess any trends in your data 
rather than taking 4 snapshots along a much larger trajectory.  You can gather 
a 
lot more detail, and very easily.  You're saving snapshots every 2 ps, which 
means you will have 2 data points that can be analyzed, rather than just 4.

> The md.mdp dile I used here is:
>
> title        = Production run for Water-POPC system
>
> ; Parameters describing the details of the NVT simulation protocol
> integrator    = md
> dt        = 0.002
> nsteps        = 500
>
> ; Parameters controlling output writing
> nstxout        = 1000
> nstvout        = 1000
> nstenergy    = 1000
> nstlog        = 1000
>
> ; Parameters describing neighbors searching and details about interaction 
> calculations
> ns_type        = grid
> nstlist        = 5
> rlist        = 1.2
> rcoulomb    = 1.2
> rvdw        = 1.2
> pbc        = xyz
>

You're using a plain cutoff for the van der Waals interactions, which is 
incorrect for the CHARMM force fields.  You need the following:

vdwtype = switch
rvdw_switch = 0.8
rvdw = 1.2
rlistlong = 1.4

The other settings are fine.

-Justin

> ; Parameters for treating bonded interactions
> continuation    = yes
> constraint_algorithm = LINCS
> constraints    = all-bonds
> lincs_iter    = 1
> lincs_order    = 4
>
> ; Parameters for treating electrostatic interactions
> coulombtype    = PME
> pme_order    = 4
> fourierspacing    = 0.16
>
> ; Temperature coupling parameters
> tcoupl        = Nose-Hoover
> tc-grps        = POPC SOL
> tau_t        = 0.5    0.5
> ref_t        = 300     300
>
> ; Pressure coupling parameters
> pcoupl        = Parrinello-Rahman
> pcoupltype    = semiisotropic
> tau_p        = 2.0
> ref_p        = 1.0    1.0
> compressibility = 4.5e-5    4.5e-5
>
>
> DispCorr    = EnerPres
> gen_vel        = no
> nstcomm        = 1
> comm_mode    = Linear
> comm_grps    =POPC SOL
>
>
>
> Sincerely,
> Shima
>
>
> 
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Sent: Friday, November 9, 2012 12:20 AM
> Subject: Re: [gmx-users] area per lipid
>
>
>
> On 11/8/12 4:39 AM, Shima Arasteh wrote:
>> Hi,
>>
>> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order 
>> to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as 
>> mentioned in articles ), I let the system to be simulated for 40 seconds. To 
>> do so, I checked the area  per lipid every 10 ns. The results of area per 
>> lipid in each step are as below:
>>
>> 1.
>> Top leaflet: 60.44
>>
>> Bottom leaflet: 59.43
>>
>>
>> 2.
>> Top leaflet: 61.135
>> Bottom leaflet: 60.11
>>
>> 3.
>> Top leaflet: 61.40
>>
>> Bottom leaflet: 60.38
>>
>> 4.
>> Top leaflet: 60.27
>>
>> Bottom leaflet: 59.27
>>
>> I expected it to approaches the expected amount steadily, but why did I get 
>> such a result? How can I get to the appropriate area  per lipid?
>>
>> Would you please give me suggestions? Any suggestions would be appreciated.
>>
>
> Without seeing a complete .mdp file, it's hard to say.  Why are you picking
> snapshots every 10 ns?  You can easily plot APL over time for the entire
> trajectory using the box vectors stored in the .edr file from (Box-X *
> Box-Y)/(number of lipids).  You would have to write your own script to do the
> calculation, but it's quite straightforward.
>
> -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] Specifying no temperature coupling in contrast to grompp output

2012-12-07 Thread Justin Lemkul




On 12/7/12 4:06 PM, Andrew DeYoung wrote:

Hi,

In my .mdp file, I set "tcoupl = no" and "pcoupl = no".  This way, I am
using the NVE ensemble.  However, when I run grompp using this .mdp file,
the grompp output includes the following line:

Number of degrees of freedom in T-Coupling group rest is 261.00

My question is, why does the grompp output refer to "T-Coupling" if I have
set "tcoupl = no"?  Does this make sense?  (I have also _not_ specified
tc_grps, tau_t, or ref_t in my .mdp file.)



More importantly, the group name specified is what is significant.  The "rest" 
group is a generic group that corresponds to everything else that is not 
actually involved.  You will see this in terms of other settings as well, like 
freeze groups or acceleration groups.


-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] Specifying no temperature coupling in contrast to grompp output

2012-12-07 Thread Andrew DeYoung

Hi,

In my .mdp file, I set "tcoupl = no" and "pcoupl = no".  This way, I am
using the NVE ensemble.  However, when I run grompp using this .mdp file,
the grompp output includes the following line:

Number of degrees of freedom in T-Coupling group rest is 261.00

My question is, why does the grompp output refer to "T-Coupling" if I have
set "tcoupl = no"?  Does this make sense?  (I have also _not_ specified
tc_grps, tau_t, or ref_t in my .mdp file.)

Thanks for your time!

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread Justin Lemkul




On 12/7/12 2:21 PM, James Starlight wrote:

Justin,

with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp

NOTE 1 [file ./mdps/em.mdp]:
   For energy conservation with switch/shift potentials, rlist should be 0.1
   to 0.3 nm larger than rvdw.

NOTE 2 [file ./mdps/em.mdp]:
   The sum of the two largest charge group radii (0.078024) is larger than
   rlist (1.20) - rvdw (1.20)



As I recall, there is a small bug where grompp ignores rlistlong when printing 
this message.  The simulation will be fine.


-Justin



Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
value because of PME) ?

2012/12/7, Justin Lemkul :



On 12/7/12 1:19 PM, James Starlight wrote:

Justin,

following to your advise I've tried to use charmm 27 ff for simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).

Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?



http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html


Does anybody know another servers for parametrization of the ligands
for charmm simulation in gromacs?



If Google can't find it, it probably doesn't exist.

-Justin


2012/12/7, Justin Lemkul :



On 12/7/12 11:42 AM, James Starlight wrote:

Justin,

ligand-only simulation in vacuum have been finished with the same
errors
:)

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   52.20.1033   0.0985  0.1000
 1  3   90.10.1168   0.1141  0.1000

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025376, max 0.140474 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   52.00.1033   0.0988  0.1000
 1  3   90.00.1168   0.1140  0.1000
step 19200, will finish Sat Dec  8 04:10:49 2012
Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052715, max 0.293316 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   49.30.0988   0.0993  0.1000
 1  3   90.00.1140   0.1293  0.1000

Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052900, max 0.294281 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   49.60.0988   0.0989  0.1000
 1  3   90.00.1140   0.1294  0.1000

Step 19202, time 38.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035783, max 0.198482 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   33.30.0989   0.0984  0.1000
 1  3   89.90.1294   0.1198  0.1000

---
Program mdrun, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176

Fatal error:
Too many LINCS warnings (1000)


ITs intresting that the same files (like step-1c_n11.pdb) have been
produced already during CG minimisation phase but the system have not
been crashed. So I suppoe that the problem is in geometry of the


If you get errors in the minimization, that should indicate that either
the

topology or configuration is flawed.


mollecule. The direct comparison of the bonds and angles with the rtp
(DGUA) is non trivial again because of differs in the file formats
representation :)



Most troubleshooting is not easy.  You can also create a topology for
DGUA
from
just about any DNA structure and compare its .top against your cGMP
topology.

-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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--


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

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread James Starlight

Justin,

with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp

NOTE 1 [file ./mdps/em.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

NOTE 2 [file ./mdps/em.mdp]:
  The sum of the two largest charge group radii (0.078024) is larger than
  rlist (1.20) - rvdw (1.20)


Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
value because of PME) ?

2012/12/7, Justin Lemkul :
>
>
> On 12/7/12 1:19 PM, James Starlight wrote:
>> Justin,
>>
>> following to your advise I've tried to use charmm 27 ff for simulation
>> of my protein-cGMP complex ( ligand was parametrized by Swiss Param
>> server).
>>
>> Could you provide me with the cut-offs for vdw as well as
>> electrostatics suitable for simulation in charmm27 and 36 force
>> fields?
>>
>
> http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
>
>> Does anybody know another servers for parametrization of the ligands
>> for charmm simulation in gromacs?
>>
>
> If Google can't find it, it probably doesn't exist.
>
> -Justin
>
>> 2012/12/7, Justin Lemkul :
>>>
>>>
>>> On 12/7/12 11:42 AM, James Starlight wrote:
 Justin,

 ligand-only simulation in vacuum have been finished with the same
 errors
 :)

 Step 19200, time 38.4 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.025443, max 0.140660 (between atoms 1 and 3)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   52.20.1033   0.0985  0.1000
 1  3   90.10.1168   0.1141  0.1000

 Step 19200, time 38.4 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.025376, max 0.140474 (between atoms 1 and 3)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   52.00.1033   0.0988  0.1000
 1  3   90.00.1168   0.1140  0.1000
 step 19200, will finish Sat Dec  8 04:10:49 2012
 Step 19201, time 38.402 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.052715, max 0.293316 (between atoms 1 and 3)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   49.30.0988   0.0993  0.1000
 1  3   90.00.1140   0.1293  0.1000

 Step 19201, time 38.402 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.052900, max 0.294281 (between atoms 1 and 3)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   49.60.0988   0.0989  0.1000
 1  3   90.00.1140   0.1294  0.1000

 Step 19202, time 38.404 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.035783, max 0.198482 (between atoms 1 and 3)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 1  2   33.30.0989   0.0984  0.1000
 1  3   89.90.1294   0.1198  0.1000

 ---
 Program mdrun, VERSION 4.5.4
 Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176

 Fatal error:
 Too many LINCS warnings (1000)


 ITs intresting that the same files (like step-1c_n11.pdb) have been
 produced already during CG minimisation phase but the system have not
 been crashed. So I suppoe that the problem is in geometry of the
>>>
>>> If you get errors in the minimization, that should indicate that either
>>> the
>>>
>>> topology or configuration is flawed.
>>>
 mollecule. The direct comparison of the bonds and angles with the rtp
 (DGUA) is non trivial again because of differs in the file formats
 representation :)

>>>
>>> Most troubleshooting is not easy.  You can also create a topology for
>>> DGUA
>>> from
>>> just about any DNA structure and compare its .top against your cGMP
>>> topology.
>>>
>>> -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
>>>
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-user

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread Justin Lemkul




On 12/7/12 1:19 PM, James Starlight wrote:

Justin,

following to your advise I've tried to use charmm 27 ff for simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).

Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?



http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html


Does anybody know another servers for parametrization of the ligands
for charmm simulation in gromacs?



If Google can't find it, it probably doesn't exist.

-Justin


2012/12/7, Justin Lemkul :



On 12/7/12 11:42 AM, James Starlight wrote:

Justin,

ligand-only simulation in vacuum have been finished with the same errors
:)

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
1  2   52.20.1033   0.0985  0.1000
1  3   90.10.1168   0.1141  0.1000

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025376, max 0.140474 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
1  2   52.00.1033   0.0988  0.1000
1  3   90.00.1168   0.1140  0.1000
step 19200, will finish Sat Dec  8 04:10:49 2012
Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052715, max 0.293316 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
1  2   49.30.0988   0.0993  0.1000
1  3   90.00.1140   0.1293  0.1000

Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052900, max 0.294281 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
1  2   49.60.0988   0.0989  0.1000
1  3   90.00.1140   0.1294  0.1000

Step 19202, time 38.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035783, max 0.198482 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
1  2   33.30.0989   0.0984  0.1000
1  3   89.90.1294   0.1198  0.1000

---
Program mdrun, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176

Fatal error:
Too many LINCS warnings (1000)


ITs intresting that the same files (like step-1c_n11.pdb) have been
produced already during CG minimisation phase but the system have not
been crashed. So I suppoe that the problem is in geometry of the


If you get errors in the minimization, that should indicate that either the

topology or configuration is flawed.


mollecule. The direct comparison of the bonds and angles with the rtp
(DGUA) is non trivial again because of differs in the file formats
representation :)



Most troubleshooting is not easy.  You can also create a topology for DGUA
from
just about any DNA structure and compare its .top against your cGMP
topology.

-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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--


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] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread James Starlight

Justin,

following to your advise I've tried to use charmm 27 ff for simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).

Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?

Does anybody know another servers for parametrization of the ligands
for charmm simulation in gromacs?

2012/12/7, Justin Lemkul :
>
>
> On 12/7/12 11:42 AM, James Starlight wrote:
>> Justin,
>>
>> ligand-only simulation in vacuum have been finished with the same errors
>> :)
>>
>> Step 19200, time 38.4 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.025443, max 0.140660 (between atoms 1 and 3)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>1  2   52.20.1033   0.0985  0.1000
>>1  3   90.10.1168   0.1141  0.1000
>>
>> Step 19200, time 38.4 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.025376, max 0.140474 (between atoms 1 and 3)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>1  2   52.00.1033   0.0988  0.1000
>>1  3   90.00.1168   0.1140  0.1000
>> step 19200, will finish Sat Dec  8 04:10:49 2012
>> Step 19201, time 38.402 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.052715, max 0.293316 (between atoms 1 and 3)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>1  2   49.30.0988   0.0993  0.1000
>>1  3   90.00.1140   0.1293  0.1000
>>
>> Step 19201, time 38.402 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.052900, max 0.294281 (between atoms 1 and 3)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>1  2   49.60.0988   0.0989  0.1000
>>1  3   90.00.1140   0.1294  0.1000
>>
>> Step 19202, time 38.404 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.035783, max 0.198482 (between atoms 1 and 3)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>1  2   33.30.0989   0.0984  0.1000
>>1  3   89.90.1294   0.1198  0.1000
>>
>> ---
>> Program mdrun, VERSION 4.5.4
>> Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176
>>
>> Fatal error:
>> Too many LINCS warnings (1000)
>>
>>
>> ITs intresting that the same files (like step-1c_n11.pdb) have been
>> produced already during CG minimisation phase but the system have not
>> been crashed. So I suppoe that the problem is in geometry of the
>
> If you get errors in the minimization, that should indicate that either the
>
> topology or configuration is flawed.
>
>> mollecule. The direct comparison of the bonds and angles with the rtp
>> (DGUA) is non trivial again because of differs in the file formats
>> representation :)
>>
>
> Most troubleshooting is not easy.  You can also create a topology for DGUA
> from
> just about any DNA structure and compare its .top against your cGMP
> topology.
>
> -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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread Justin Lemkul




On 12/7/12 11:42 AM, James Starlight wrote:

Justin,

ligand-only simulation in vacuum have been finished with the same errors :)

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   1  2   52.20.1033   0.0985  0.1000
   1  3   90.10.1168   0.1141  0.1000

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025376, max 0.140474 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   1  2   52.00.1033   0.0988  0.1000
   1  3   90.00.1168   0.1140  0.1000
step 19200, will finish Sat Dec  8 04:10:49 2012
Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052715, max 0.293316 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   1  2   49.30.0988   0.0993  0.1000
   1  3   90.00.1140   0.1293  0.1000

Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052900, max 0.294281 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   1  2   49.60.0988   0.0989  0.1000
   1  3   90.00.1140   0.1294  0.1000

Step 19202, time 38.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035783, max 0.198482 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   1  2   33.30.0989   0.0984  0.1000
   1  3   89.90.1294   0.1198  0.1000

---
Program mdrun, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176

Fatal error:
Too many LINCS warnings (1000)


ITs intresting that the same files (like step-1c_n11.pdb) have been
produced already during CG minimisation phase but the system have not
been crashed. So I suppoe that the problem is in geometry of the


If you get errors in the minimization, that should indicate that either the 
topology or configuration is flawed.



mollecule. The direct comparison of the bonds and angles with the rtp
(DGUA) is non trivial again because of differs in the file formats
representation :)



Most troubleshooting is not easy.  You can also create a topology for DGUA from 
just about any DNA structure and compare its .top against your cGMP topology.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread James Starlight

Justin,

ligand-only simulation in vacuum have been finished with the same errors :)

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2   52.20.1033   0.0985  0.1000
  1  3   90.10.1168   0.1141  0.1000

Step 19200, time 38.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025376, max 0.140474 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2   52.00.1033   0.0988  0.1000
  1  3   90.00.1168   0.1140  0.1000
step 19200, will finish Sat Dec  8 04:10:49 2012
Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052715, max 0.293316 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2   49.30.0988   0.0993  0.1000
  1  3   90.00.1140   0.1293  0.1000

Step 19201, time 38.402 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052900, max 0.294281 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2   49.60.0988   0.0989  0.1000
  1  3   90.00.1140   0.1294  0.1000

Step 19202, time 38.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035783, max 0.198482 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2   33.30.0989   0.0984  0.1000
  1  3   89.90.1294   0.1198  0.1000

---
Program mdrun, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176

Fatal error:
Too many LINCS warnings (1000)


ITs intresting that the same files (like step-1c_n11.pdb) have been
produced already during CG minimisation phase but the system have not
been crashed. So I suppoe that the problem is in geometry of the
mollecule. The direct comparison of the bonds and angles with the rtp
(DGUA) is non trivial again because of differs in the file formats
representation :)


James

2012/12/7 Justin Lemkul :
>
>
> On 12/7/12 10:41 AM, James Starlight wrote:
>>
>> Today I've tried to simulate complexes of my protein with the cyclic
>> GMP parametrized by ATB's. (below the recent parametrisation for
>> charges of that molecule done by am1 algorithm)
>>
>> [ moleculetype ]
>> ; Name   nrexcl
>> _N4P 3
>> [ atoms ]
>> ;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
>>  1NT1_N4P N21   -0.848  14.0067
>>  2 H1_N4PH2210.424   1.0080
>>  3 H1_N4PH2110.424   1.0080  ;  0.000
>>  4NR1_N4P N12   -0.684  14.0067
>>  5 H1_N4P H120.437   1.0080
>>  6 C1_N4P C220.779  12.0110
>>  7NR1_N4P N32   -0.678  14.0067
>>  8 C1_N4P C420.440  12.0110
>>  9NR1_N4P N92   -0.294  14.0067  ;  0.000
>> 10 C1_N4P C830.272  12.0110
>> 11HC1_N4PH0130.141   1.0080
>> 12 O1_N4P O63   -0.555  15.9994
>> 13 C1_N4P C630.608  12.0110
>> 14 C1_N4P C530.101  12.0110
>> 15NR1_N4P N73   -0.567  14.0067  ;  0.000
>> 16OE1_N4PO4*4   -0.451  15.9994
>> 17   CH11_N4PC1*40.451  13.0190  ;  0.000
>> 18OA1_N4PO5*5   -0.394  15.9994
>> 19 P1_N4PPAQ50.974  30.9738
>> 20OM1_N4POAR5   -0.616  15.9994
>> 21OA1_N4PO3*5   -0.390  15.9994
>> 22OA1_N4POAS5   -0.584  15.9994
>> 23 H1_N4PH0350.491   1.0080
>> 24   CH21_N4PC5*50.281  14.0270
>> 25   CH11_N4PC4*50.238  13.0190  ;  0.000
>> 26   CH11_N4PC3*60.000  13.0190  ;  0.000
>> 27   CH11_N4PC2*70.181  13.0190
>> 28OA1_N4PO2*7   -0.645  15.9994
>> 29 H1_N4PH8M70.464   1.0080  ;  0.000
>>
>> In all cases my system have always been crushed after equilibration
>> run ( during that phase with the posres applied on both protein as
>> well as ligand the system was stabile) with the errors like
>>
>> Step 19, time 0.038 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 1.203662, max 11.750027 (between atoms 4289 an

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread Justin Lemkul




On 12/7/12 10:41 AM, James Starlight wrote:

Today I've tried to simulate complexes of my protein with the cyclic
GMP parametrized by ATB's. (below the recent parametrisation for
charges of that molecule done by am1 algorithm)

[ moleculetype ]
; Name   nrexcl
_N4P 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
 1NT1_N4P N21   -0.848  14.0067
 2 H1_N4PH2210.424   1.0080
 3 H1_N4PH2110.424   1.0080  ;  0.000
 4NR1_N4P N12   -0.684  14.0067
 5 H1_N4P H120.437   1.0080
 6 C1_N4P C220.779  12.0110
 7NR1_N4P N32   -0.678  14.0067
 8 C1_N4P C420.440  12.0110
 9NR1_N4P N92   -0.294  14.0067  ;  0.000
10 C1_N4P C830.272  12.0110
11HC1_N4PH0130.141   1.0080
12 O1_N4P O63   -0.555  15.9994
13 C1_N4P C630.608  12.0110
14 C1_N4P C530.101  12.0110
15NR1_N4P N73   -0.567  14.0067  ;  0.000
16OE1_N4PO4*4   -0.451  15.9994
17   CH11_N4PC1*40.451  13.0190  ;  0.000
18OA1_N4PO5*5   -0.394  15.9994
19 P1_N4PPAQ50.974  30.9738
20OM1_N4POAR5   -0.616  15.9994
21OA1_N4PO3*5   -0.390  15.9994
22OA1_N4POAS5   -0.584  15.9994
23 H1_N4PH0350.491   1.0080
24   CH21_N4PC5*50.281  14.0270
25   CH11_N4PC4*50.238  13.0190  ;  0.000
26   CH11_N4PC3*60.000  13.0190  ;  0.000
27   CH11_N4PC2*70.181  13.0190
28OA1_N4PO2*7   -0.645  15.9994
29 H1_N4PH8M70.464   1.0080  ;  0.000

In all cases my system have always been crushed after equilibration
run ( during that phase with the posres applied on both protein as
well as ligand the system was stabile) with the errors like

Step 19, time 0.038 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.203662, max 11.750027 (between atoms 4289 and 4287)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
4288   4287   89.50.2277   1.1291  0.1000
4292   4287   90.50.1304   0.9898  0.1350
4289   4287   90.40.1056   1.2750  0.1000
4318   4303   30.80.1531   0.1816  0.1530
4304   4303   45.20.1097   0.1531  0.1090
4309   4310   90.00.2629   0.3419  0.1000
4299   4290   84.20.1404   0.1641  0.1400
4292   4290   89.40.1362   0.5025  0.1380
4291   4290   89.20.1563   0.2142  0.1000
4293   4292   89.10.1252   0.5682  0.1320
4294   4293   78.10.1387   0.3906  0.1350
4300   4294   92.20.1385   0.4639  0.1390
4295   4294   91.10.1365   0.5711  0.1380
4303   4295   43.40.1482   0.1954  0.1470
4296   4295   36.60.1408   0.1593  0.1400
4301   4296   89.90.1323   0.5162  0.1320
4297   4296   32.50.1089   0.1343  0.1090
4299   4298   87.00.1230   0.2758  0.1230
4300   4299   89.80.1431   0.5922  0.1430
4301   4300   79.00.1381   0.1928  0.1380


Fatal error:
1 particles communicated to PME node 26 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS

After that my system have been crashed and than produced many
step*.pdb files in the work dirr.

It's intresting that with the prodrg topology of that mollecule ( with
worst charge distribution) I've never such problems. Might that error
be due to the wrong geometry parametrisation (e.g incorect dihedrals)
of the cGMP made by ATB ?



Simulate all components of your system separately and follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. 
 Dihedrals should not be a major issue, since all of them can be adequately 
described by those already present in the parent force field.  Check against DGUA.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.or

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

2012-12-07 Thread James Starlight

Today I've tried to simulate complexes of my protein with the cyclic
GMP parametrized by ATB's. (below the recent parametrisation for
charges of that molecule done by am1 algorithm)

[ moleculetype ]
; Name   nrexcl
_N4P 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1NT1_N4P N21   -0.848  14.0067
2 H1_N4PH2210.424   1.0080
3 H1_N4PH2110.424   1.0080  ;  0.000
4NR1_N4P N12   -0.684  14.0067
5 H1_N4P H120.437   1.0080
6 C1_N4P C220.779  12.0110
7NR1_N4P N32   -0.678  14.0067
8 C1_N4P C420.440  12.0110
9NR1_N4P N92   -0.294  14.0067  ;  0.000
   10 C1_N4P C830.272  12.0110
   11HC1_N4PH0130.141   1.0080
   12 O1_N4P O63   -0.555  15.9994
   13 C1_N4P C630.608  12.0110
   14 C1_N4P C530.101  12.0110
   15NR1_N4P N73   -0.567  14.0067  ;  0.000
   16OE1_N4PO4*4   -0.451  15.9994
   17   CH11_N4PC1*40.451  13.0190  ;  0.000
   18OA1_N4PO5*5   -0.394  15.9994
   19 P1_N4PPAQ50.974  30.9738
   20OM1_N4POAR5   -0.616  15.9994
   21OA1_N4PO3*5   -0.390  15.9994
   22OA1_N4POAS5   -0.584  15.9994
   23 H1_N4PH0350.491   1.0080
   24   CH21_N4PC5*50.281  14.0270
   25   CH11_N4PC4*50.238  13.0190  ;  0.000
   26   CH11_N4PC3*60.000  13.0190  ;  0.000
   27   CH11_N4PC2*70.181  13.0190
   28OA1_N4PO2*7   -0.645  15.9994
   29 H1_N4PH8M70.464   1.0080  ;  0.000

In all cases my system have always been crushed after equilibration
run ( during that phase with the posres applied on both protein as
well as ligand the system was stabile) with the errors like

Step 19, time 0.038 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.203662, max 11.750027 (between atoms 4289 and 4287)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4288   4287   89.50.2277   1.1291  0.1000
   4292   4287   90.50.1304   0.9898  0.1350
   4289   4287   90.40.1056   1.2750  0.1000
   4318   4303   30.80.1531   0.1816  0.1530
   4304   4303   45.20.1097   0.1531  0.1090
   4309   4310   90.00.2629   0.3419  0.1000
   4299   4290   84.20.1404   0.1641  0.1400
   4292   4290   89.40.1362   0.5025  0.1380
   4291   4290   89.20.1563   0.2142  0.1000
   4293   4292   89.10.1252   0.5682  0.1320
   4294   4293   78.10.1387   0.3906  0.1350
   4300   4294   92.20.1385   0.4639  0.1390
   4295   4294   91.10.1365   0.5711  0.1380
   4303   4295   43.40.1482   0.1954  0.1470
   4296   4295   36.60.1408   0.1593  0.1400
   4301   4296   89.90.1323   0.5162  0.1320
   4297   4296   32.50.1089   0.1343  0.1090
   4299   4298   87.00.1230   0.2758  0.1230
   4300   4299   89.80.1431   0.5922  0.1430
   4301   4300   79.00.1381   0.1928  0.1380


Fatal error:
1 particles communicated to PME node 26 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS

After that my system have been crashed and than produced many
step*.pdb files in the work dirr.

It's intresting that with the prodrg topology of that mollecule ( with
worst charge distribution) I've never such problems. Might that error
be due to the wrong geometry parametrisation (e.g incorect dihedrals)
of the cGMP made by ATB ?


James

2012/12/6 James Starlight :
> Justin,
>
> Thanks again for explanation.
>
>
> It's interesting that above parametrization made by ATB have cased the
> system to crash within first ps of modeling ;) (On the contrarythe
> system with the ligand made by prodrg have been very stable during
> 100ns). I ve tried to re-parametrized my molecule by another algorithm
> implemented in ATB ( am1 instead of pm3 which was used in the crashed
> simulation).
>
>
> James
>
> 2012/12/6, Justin Lemkul :
>>
>>
>> On 12/6/12 2:39 AM, James Starlight wrote:
>>> Justin,
>>>
>>> Could you provide me with the example of the server where I could
>>> obtain Gromac's itp topologies for the charmm ff? I know many such
>>> servers which could be useful only for preparation systems for NAMD
>>> program.
>>>
>>
>> Google "CHARMM ligand topology in Gromacs" (without the qu

[gmx-users] Extending REMD simulations problem

2012-12-07 Thread Kenny Bravo Rodriguez


Hi all,

i want to extend a remd simulation that finished correctly, but i always 
get the same segmentation fault error.

This is what i am doing with a test system.

I run the REMD simulation with:

mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500

After the simulation correctly finished i extend the number of time 
steps in each .tpr file with:


tpbconv_d -s test_1.tpr -extend 20 -o testl_1.tpr
tpbconv_d -s test_0.tpr -extend 20 -o testl_0.tpr

And then i try to continue the REMD simulation with:

mdrun_mpi_d -s testl_.tpr -deffnm test_ -cpi test_.cpt -multi 2 -replex 500

but i only got the error message show below.

What am i doing wrong?

Thanks in advanced
Kenny

NNODES=6, MYRANK=1, HOSTNAME=hydra02
NNODES=6, MYRANK=3, HOSTNAME=hydra02
NNODES=6, MYRANK=4, HOSTNAME=hydra02
NNODES=6, MYRANK=0, HOSTNAME=hydra02
NODEID=0 argc=11
NODEID=1 argc=11
NODEID=4 argc=11
 :-)  G  R  O  M  A  C  S  (-:

NNODES=6, MYRANK=5, HOSTNAME=hydra02
NODEID=5 argc=11
  GROningen Mixture of Alchemy and Childrens' Stories

:-)  VERSION 4.5.5  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
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.

:-)  mdrun_mpi_d (double precision)  (-:

NNODES=6, MYRANK=2, HOSTNAME=hydra02
NODEID=2 argc=11
NODEID=3 argc=11
node 0 par_fn 'testl_0.tpr'
node 0 par_fn 'test_0.trr'
node 0 par_fn 'test_0.xtc'
node 0 par_fn 'test_0.cpt'
node 0 par_fn 'test_0.cpt'
node 0 par_fn 'test_0.gro'
node 0 par_fn 'test_0.edr'
Option Filename  Type Description

  -s testl_.tpr  InputRun input file: tpr tpb tpa
  -o  test_.trr  Output   Full precision trajectory: trr trj cpt
  -x  test_.xtc  Output, Opt. Compressed trajectory (portable xdr 
format)

-cpi  test_.cpt  Input, Opt!  Checkpoint file
-cpo  test_.cpt  Output, Opt. Checkpoint file
  -c  test_.gro  Output   Structure file: gro g96 pdb etc.
  -e  test_.edr  Output   Energy file
  -g  test_.log  Output   Log file
-dhdl test_.xvg  Output, Opt. xvgr/xmgr file
-fieldtest_.xvg  Output, Opt. xvgr/xmgr file
-tabletest_.xvg  Input, Opt.  xvgr/xmgr file
-tablep   test_.xvg  Input, Opt.  xvgr/xmgr file
-tableb   test_.xvg  Input, Opt.  xvgr/xmgr file
-reruntest_.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi  test_.xvg  Output, Opt. xvgr/xmgr file
-tpid test_.xvg  Output, Opt. xvgr/xmgr file
 -ei  test_.edi  Input, Opt.  ED sampling input
 -eo  test_.edo  Output, Opt. ED sampling output
  -j  test_.gct  Input, Opt.  General coupling stuff
 -jo  test_.gct  Output, Opt. General coupling stuff
-ffouttest_.xvg  Output, Opt. xvgr/xmgr file
-devout   test_.xvg  Output, Opt. xvgr/xmgr file
-runavtest_.xvg  Output, Opt. xvgr/xmgr file
 -px  test_.xvg  Output, Opt. xvgr/xmgr file
 -pf  test_.xvg  Output, Opt. xvgr/xmgr file
-mtx  test_.mtx  Output, Opt. Hessian matrix
 -dn  test_.ndx  Output, Opt. Index file
-multidir test_  Input, Opt., Mult. Run directory

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string test_   Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or 
cartesian

-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions 
with
DD (nm), 0 is determine from initial 
coordinates

-rconreal   0

Re: [gmx-users] Installation Error

2012-12-07 Thread Mark Abraham

See
http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite

On Fri, Dec 7, 2012 at 9:08 AM, BHARATI DUTTA wrote:

>
> Hi Justin,
>
> I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but
> I am getting an error. The error message is attached in the mail in a text
> file "Installation_error.txt".
>
> I have installed fftw-3.3.3 in my system.
>
> I have checked threads on the mailing list which have reported the same
> error and have also followed whatever solution has been provided but
> unfortunately its still not successful. Now I am at a fix 
> Could you please suggest me what should I do next for successfully
> installing gromacs on my machine? could it be some compatibilty issue or m
> I missing out something crucial?
>
>
> - Bharati
>--
>  *Bharati Dutta*
> Research Associate
> Discovery Informatics *Piramal Life Sciences 
> Limited*
> 1, Nirlon Complex,
> Goregaon Link Road,
> Goregaon(E)
> Mumbai, Maharashtra 400 063
> India *bharati.du...@piramal.com* 
>
>
>   --
>
> This communication may contain information that is proprietary
> confidential or exempt from disclosure. If you are not the intended
> recipient please note that any other dissemination distribution use or
> copying of this communication is strictly prohibited. Anyone who receives
> this message in error should notify the sender immediately by telephone or
> by return e-mail and delete it from his or her computer.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Fwd: [gmx-developers] cmake bug when install GMX 4.6 beta2

2012-12-07 Thread Mark Abraham

Hi Yukun,

In future, please only target email associated with GROMACS development to
the gmx-developers mailing list. gmx-users is for usage questions, such as
installation issues. I am replying to this email to both lists.

If you've correctly installed and used icc 11.1, then I think you should
not have this problem. Try a full-qualified path to icc - I don't know if
your use of CMAKE_PREFIX_PATH is sufficient there - and IIRC if you have
sourced the environment script that comes with Intel's compilers then you
should not need to touch CMAKE_PREFIX_PATH for the compiler. The compiler
diagnosis is at the very top of the cmake output, so please look there for
clues.

Mark

-- Forwarded message --
From: Yorquant Wang 
Date: Fri, Dec 7, 2012 at 9:18 AM
Subject: [gmx-developers] cmake bug when install GMX 4.6 beta2
To: Discussion list for GROMACS development 


Hi all:
   I am trying to install GMX 4.6 beta2 on a highly paralleled server.
  with cmake  version 2.8.4
   MPIopenmpi-144 compiled with intel 11.1 compiler
   fftw 3.3.2
   compiler  intel 11.1 gcc 4.1.2
   CPU  Intel(R) Xeon(R)  E5450 with 8cores in one node, with
infinited band node communication.
   with the compling commend:

 # 
CMAKE_PREFIX_PATH=/home/software/openmpi-144-intel-11-1:/home/dw11-sg007/dying/fftw3
CC=icc  /home/software/cmake-2.8.4/bin/cmake ..
then I got such a error :

   CMake Warning at CMakeLists.txt:733 (message):
   No C SSE4.1 flag found.  Consider a newer compiler, or
disable SSE4.1 for slightly lower performance.
   CMake Error at CMakeLists.txt:756 (message):
   Cannot find smmintrin.h, which is required for SSE4.1
intrinsics support.
  Is there anybody knowing how to handle such a problem?  Thank you very
much !

Best

-- 
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai

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Re: [gmx-users] GROMACS 4.6-beta2 released

2012-12-07 Thread Mark Abraham

Speed-up depends what you measure against, what precision GROMACS is using,
and what your AVX hardware is. There is no single number worth mentioning.
GROMACS has different AVX kernels for single vs double, and Intel Sandy
Bridge / Ivy Bridge vs AMD's Opteron / Bulldozer. I haven't seen any
numbers because the author of the kernels hasn't produced them yet, but
they will be considerably faster than anything you might compare them with.

Mark

On Fri, Dec 7, 2012 at 4:37 AM, Yorquant Wang  wrote:

> Hi Roland:
>  Based on your test, how many speed-up you get?
> Yorquant
>
> 2012/12/7 Roland Schulz 
>
> > On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang 
> wrote:
> >
> > > Hi Mark:
> > > There is a new instruction set architecture (*Advanced Vector
> > > Extensions
> > > * (AVX)) that can make float calculation in Intel CPU faster two times
> > > compared with the old instruction set. I want to know if the Gromacs
> > > developers have a plan to make GMX support AVX. if the GMX can support
> > GMX,
> > > I think maybe two times speed-up in GMX will be gotten immediately.
> > >
> > Yes AVX is supported. But you won't see a 2x speedup.
> >
> > Roland
> >
> >
> > >
> > >   Best
> > >
> > > Yukun Wang
> > > PhD candidate
> > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> > > Tong University
> > > Cell phone: 13621806236.
> > > China Shanghai
> > >
> > >
> > > 2012/12/7 Mark Abraham 
> > >
> > > > Hi all,
> > > >
> > > > We've updated the GROMACS beta version to fix some bugs both you and
> we
> > > > found. We've also added the Adaptive resolution scheme (adResS) to
> our
> > > list
> > > > of new features (though we still have yet to publish a complete list
> of
> > > > those!). adResS couples two systems with different resolutions by a
> > force
> > > > interpolation, which can be used to speed-up atomistic simulations.
> The
> > > new
> > > > source package can be found at
> > > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6-beta2.tar.gz.
> > Installation
> > > > instructions still here
> > > > http://www.gromacs.org/Documentation/Installation_Instructions
> > > >
> > > > Please try it out, particularly if you haven't done so already! Also,
> > if
> > > > everything is smooth sailing, please drop us a line on gmx-users just
> > to
> > > > say that. We can't tell whether silence is "worked great, nothing to
> > say"
> > > > or "haven't tried it yet". That will help us judge when things are
> > stable
> > > > enough to make a real release!
> > > >
> > > > Speaking of that, we are keen to make that final release soon. While
> we
> > > > can't pick a date yet, we promise that if you give us feedback by
> > > December
> > > > 21, then we will make a sincere effort to incorporate the results of
> > that
> > > > feedback in the final release. In particular, if it's an issue on our
> > > > Redmine bug report database http://redmine.gromacs.org, then it will
> > be
> > > > sure to get our attention and consideration. You'll need to register
> an
> > > > account to make a bug report (so that we can get back to you), but
> > that's
> > > > free and easy.
> > > >
> > > > We hope to release a current version of our regression test suite
> next
> > > > week, and a benchmark set soon.
> > > >
> > > > Cheers,
> > > >
> > > > Mark Abraham
> > > > GROMACS development manager
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > >
> > >
> > >
> > > --
> > > Yukun Wang
> > > PhD candidate
> > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> > > Tong University
> > > Cell phone: 13621806236.
> > > China Shanghai
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > >
> > >
> > >
> > >
> >
> >
> > --
> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> > 865-241-1537, ORNL PO BOX 2008 MS6309
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > * Can't post? Read http://www.grom

[gmx-users] Installation Error

2012-12-07 Thread BHARATI DUTTA

Hi Justin,

I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but 
I am getting an error. The error message is attached in the mail in a text 
file "Installation_error.txt".

I have installed fftw-3.3.3 in my system.

I have checked threads on the mailing list which have reported the same 
error and have also followed whatever solution has been provided but 
unfortunately its still not successful. Now I am at a fix 
Could you please suggest me what should I do next for successfully 
installing gromacs on my machine? could it be some compatibilty issue or m 
I missing out something crucial?


- Bharati


Bharati Dutta
Research Associate
Discovery Informatics
Piramal Life Sciences Limited
1, Nirlon Complex,
Goregaon Link Road,
Goregaon(E)
Mumbai, Maharashtra 400 063
India
bharati.du...@piramal.com





This communication may contain information that is proprietary 
confidential or exempt from disclosure. If you are not the intended 
recipient please note that any other dissemination distribution use or 
copying of this communication is strictly prohibited. Anyone who receives 
this message in error should notify the sender immediately by telephone or 
by return e-mail and delete it from his or her computer. 

/usr/bin/ld: /usr/local/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 
against `a local symbol' can not be used when making a shared object; recompile 
with -fPIC
/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/home/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1
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Re: [gmx-users] area per lipid

Re: [gmx-users] Specifying no temperature coupling in contrast to grompp output

[gmx-users] Specifying no temperature coupling in contrast to grompp output

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[gmx-users] Extending REMD simulations problem

Re: [gmx-users] Installation Error

[gmx-users] Fwd: [gmx-developers] cmake bug when install GMX 4.6 beta2

Re: [gmx-users] GROMACS 4.6-beta2 released

[gmx-users] Installation Error

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