[gmx-users] Fw: ionic liquids

[Prema Awati]

 








-- Original Message --

From: prem...@iiserpune.ac.in

To: vvcha...@gmail.com

Date: Mon, 2 May 2011 11:29:44 +0530 (GMT+05:30)

Subject: ionic liquids



sir,

I am grateful regarding your reply. The 
reported density for [bmim][bf4] system is 1.198 g/cm3.I was wondering whether 
you asked for the topology that I am using for my calculation or the one that 
Tsuzuki.et.al.(one I am referring) have used. Well, following is the toopology 
that I have created for my system.





; File 'bmim.top' was generated

; By user: onbekend (0)

; On host: onbekend

; At date: Fri Apr 15 18:03:14 2011

;

; This is a include topology file

;

; It was generated using program:

; Generated by x2top

;

; Command line was:

; g_x2top_d -f boxbmim.pdb -o bmim.top

;

; Force field was read from the standard 
Gromacs share directory.

;



; Include forcefield parameters

#include "oplsaa.ff/forcefield.itp"



[ moleculetype ]

; Name nrexcl

BIM 3



[ atoms ]

; nr type resnr residue atom cgnr charge mass 
typeB chargeB massB

1 opls_557 1 BIM NA 1 0.24 14.0067 ; qtot 0.24

2 opls_560 1 BIM CW 2 -0.16 12.011 ; qtot 0.74

3 opls_561 1 BIM CW 3 -0.27 12.011 ; qtot 1.24

4 opls_557 1 BIM NA 4 0.32 14.0067 ; qtot 1.48

5 opls_558 1 BIM CR 5 -0.22 12.011 ; qtot 1.26

6 opls_905 1 BIM C1 6 -0.35 12.011 ; qtot 0.91

7 opls_908 1 BIM C1 7 -0.14 12.011 ; qtot 0.77

8 opls_136 1 BIM C2 8 -0.12 12.011 ; qtot 0.65

9 opls_136 1 BIM CS 9 -0.12 12.011 ; qtot 0.53

10 opls_135 1 BIM CT 10 -0.18 12.011 ; qtot 0.35

11 opls_565 1 BIM HA 2 0.23 1.008 ; qtot 0.41

12 opls_564 1 BIM HA 3 0.27 1.008 ; qtot 0.47

13 opls_563 1 BIM HA 5 0.25 1.008 ; qtot 0.53

14 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.59

15 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.65

16 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.71

17 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.77

18 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.83

19 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.89

20 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.95

21 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.01

22 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.07

23 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.13

24 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.19

25 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.25



[ bonds ]

; ai aj funct c0 c1 c2 c3

1 2 1 0.1372 178656.8

1 5 1 0.1340 199576.8

1 6 1 0.1466 141000.8

2 3 1 0.1375 217568.0

2 11 1 0.1080 138490.4

3 4 1 0.1372 178656.8

3 12 1 0.1080 138490.4

4 5 1 0.1340 199576.8

4 7 1 0.1466 141000.8

5 13 1 0.1080 138490.4

6 14 1 0.1090 138490.4

  

[gmx-users] Continuation=yes From?

[mohsen ramezanpour]

Dear Dr.Justin

Regarding Umbrella Sampling tutorial:

The CONTINUATION option in md_umbrella.mdp is YES,
and you have noticed : From NPT

I can't understand it's reason correctly!

we run a NPT and then Pulling, then extracted some configurations from
pull.trr file.
I think we must continue from pull.cptnot   NPT.cpt

I mean :
grompp   -f  md_umbrella.mdp .  -t   pull.cpt
is more correct than

grompp-f md_umbrella.mdp .. -t  NPT.cpt

am I right?
Thanks in advance for your reply
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[gmx-users] reg lincs error and exploding problem during mdrun

[vidhya sankar]

Thanks Justin,
  now i have different problem when i run mdrun_d programme 
with the following command 
 ./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr  -c 1HHO_md.gro -e md.edr -nt 1
i got error as follows
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.348354, max 2.293388 (between atoms 27 and 28)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 45 47   30.1    0.1250   0.0966  0.1250
 45 46   89.4    0.1250   0.1611  0.1250
 44 45   38.0    0.1530   0.1715  0.1530
 36 37   89.8    0.1090   0.1977  0.1090
 27 28   89.6    0.1090   0.3590  0.1090
 18 19   89.1    0.1090   0.1375  0.1090
 15 17   56.1    0.1250   0.1306  0.1250
  6  7   89.2    0.1090   0.1781  0.1090
Wrote pdb files with previous and current coordinates

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 6.925181, max 29.122365 (between atoms 9 and 10)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 45 47   95.4    0.0966   0.1734  0.1250
 36 37   90.1    0.1977   1.6174  0.1090
 27 28   90.1    0.3590   0.1991  0.1090
 18 20   61.3    0.1422   0.0426  0.1400
 18 19   91.3    0.1375   0.2554  0.1090
 15 17   89.4    0.1306   0.1306  0.1250
 11 18   86.8    0.1423   0.2272  0.1400
 10 12   90.0    0.1542   4.1927  0.1530
 10 11   89.4    0.1418   4.2147  0.1400
  9 13   36.9    0.1545   0.2135  0.1530
  9 10   89.3    0.1415   4.2171  0.1400
  8  9   39.6    0.1422   0.1957  0.1400
  6  7   89.3    0.1781   0.2107  0.1090
  2 11   87.7    0.1404   0.2813  0.1380
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 10 and 14 at distance 4.309 which is larger 
than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1141861312104.288574, max 8387384410969.760742 (between atoms 36 and 37)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2  114.2    0.2088 307491611.7030  0.2000
 44 45   41.6    0.1457   0.1972  0.1530
 43 44  129.5    0.1536 16995520.2978  0.1530
 40 43  100.2    0.1544 526802811.8353  0.1530
 40 41  115.4    0.1427 1126735523.3763  0.1400
 39 42  110.6    0.1546 3296841333.8448  0.1530
 39 40   95.3    0.1427 3867105914.6031  0.1400
 38 39  103.0    0.1432 6773859895.7491  0.1400
 36 38   97.4    0.1419 20921022161.9095  0.1400
 36 37   89.9    1.6174 914224900795.8143  0.1090
 34 35  105.4    0.1340 772011346.9170  0.1340
 32 36   97.9    0.1434 21005542749.8526  0.1400
 31 34  103.2    0.1533 4047716956.2246  0.1530
 31 32  100.6    0.1407 6865225352.3692  0.1400
 30 33  108.3    0.1530 640798229.9764  0.1530
 30 31   99.0    0.1401 4174186935.5429  0.1400
 29 30  120.6    0.1399 992312479.3422  0.1400
 27 29  111.0    0.1429 1205532064.0067  0.1400
 27 28  121.7    0.1991 412296837.5467  0.1090
 25 26   78.4    0.1354   5.1420  0.1340
 23 27   97.8    0.1457 412296831.0029  0.1400
 22 25  106.1    0.1565  14.5779  0.1530
 22 23   81.6    0.1448  15.7238  0.1400
 21 24   98.1    0.1614   4.0101  0.1530
 21 22   88.5    0.1472  15.3081  0.1400
 20 21   95.2    0.1568  14.5247  0.1400
 18 20   84.5    0.0426  15.1546  0.1400
 18 19   90.3    0.2554   3.8535  0.1090
 15 17   89.9    0.1306   4.2160  0.1250
 15 16   90.0    0.1191  25.1978  0.1250
 14 15   88.7    0.1553   3.4423  0.1530
 13 14   97.9    0.1679   2.7244  0.1530
 11 18   76.7    0.2272  23.5748  0.1400
 10 12  170.5    4.1927  15.3594  0.1530
 10 11  126.4    4.2147  26.6521  0.1400
  9 13   51.9    0.2135   3.3106  0.1530
  9 10  165.5    4.2171  16.1115  0.1400
  8  9   76.6    0.1957   7.1674  0.1400
  6 41  109.4    0.1477 1166436972.1222  0.1400
  6  8  117.5    0.1602 406664611.1456  0.1400
  6  7  135.7    0.2107 406664648.5804  0.1090
  5 41  115.5    0.1408 3655729543.2299  0.1380
  5 38  106.1    0.1421 6636732910.3252  0.1380
  4 32  105.3    

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

[Mark Abraham]

On 1/05/2011 11:48 PM, Faezeh Kargar wrote:


Thank you very much for your reply. could you please tell me if there 
is any way to solve this problem and restart running the code?




If my theory is right, keep using the same installation of GROMACS 4.5. 
Talk to whoever manages your system about what may have happened. I'm 
not going to keep re-iterating my guess or predicating further 
discussion upon it :-)


Mark


Karagr


> On 30/04/2011 11:37 PM, Faezeh Kargar wrote:
>>
>>
>> > On 4/30/2011 7:22 PM, Faezeh Kargar wrote:
>> >>
>> >> Dear gmx users,
>> >>
>> >> My code stops running because of electricity voltage oscillation. it
>> >> happened for several times and each time I restarted running my 
code.

>> >> but for this time with command
>> >>
>> >> mdrun -s topol.tpr -x
>> >> traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt
>> >> -e ener.part0002.part0003.part0004.part0004.part0005.edr -g
>> >> md.part0002.part0003.part0004.part0004.part0005.log &
>> >>
>> >> I used this command before without any error. but now I encountered
>> >> error like this:
>> >>
>> >>
>> >> Program mdrun, VERSION 4.0.7
>> >> Source
>> >> code file: checkpoint.c, line: 565
>> >>
>> >> Fatal error:
>> >> Attempting
>> >> to read a checkpoint file of version 12 with code of version 4
>> >>
>> >> I looked at the file "checkpoint.c". at first the version of
>> >> checkpoint file is 4 but I do not know how and why it changes.
>> >>
>> >
>> > The usual reason for this kind of error is that you're using an old
>> > version of GROMACS to access a file written by a new version. That's
>> not
>> > a good idea.
>> >
>> > Mark
>> >
>>
>> Thank you for your reply. I just use version 4.0.7 of GROMACS and all
>> of files are written by this version. as I said before, I could
>> restart running of my codes with this command without any problem.
>>
>
> Version 12 is that used in 4.5.x, so I think you are using that version.
> Someone may have changed the software and not told you about it (in
> which case, tell them to stop wasting people's time). Or you've migrated
> files from one place to another, or something similar.
>
> Mark
> --
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>


--
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Re: [gmx-users] Re: Simluations in vacuum - energy increase

[Mark Abraham]

On 2/05/2011 4:00 AM, Zoe Hall wrote:

Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says 
"hbonds", not "h-bonds", however didn't make much difference which one I used.


"h-bonds" is correct. The manual's been wrong for nearly a decade(!). 
I've fixed it.


Mark
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Re: [gmx-users] Source Code for Lennard jones truncation schemes

[Mark Abraham]

On 2/05/2011 6:31 AM, Apoorv Kalyankar wrote:

Hello,

I was wondering where can I find the source code where the different
cut-off schemes (cut-off, shift, switch etc) for lennard jones
interactions have been implemented.
Thanks.


See src/gmxlib/nonbonded/nb_kerneltype.h and files in 
src/gmxlib/nonbonded/nb_kernel_c (especially nb_kernel010.c). The 
non-plain-cutoff schemes are actually implemented with table lookups, 
see src/mdlib/tables.c for their construction.


Mark
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Re: [gmx-users] Re: Simluations in vacuum - energy increase

[Erik Marklund]

David van der Spoel skrev 2011-05-01 20.10:

On 2011-05-01 20.00, Zoe Hall wrote:
Hi - thanks - much improved with shorter timestep and increase in 
constraint accuracy. Manual says "hbonds", not "h-bonds", however 
didn't make much difference which one I used. Could someone suggest 
the reason why you would want to turn temperature coupling off during 
the simulations - I don't really understand this.


In our work we want to study evaporation and cooling induced by the 
leaving water molecules. If you don't have water molecules, or even 
assume some kind of heat bath (e.g. a gas atmosphere), you could turn 
on T-coupling.
We furthermore managed to simulate lysozyme in vacuo with 1 fs time 
steps, without energy drift. See Marklund et. al. PCCP v. 11:36, pp. 
7741 (2009) for clues.

Thanks,

Zoe

On 2011-04-30 14.17, Zoe Hall wrote:

Gmx-users,

I am trying to carry out a simulation of lysozyme in vacuo using the
OPLS-AA forcefield. After energy minimisation, the protein is run for
10ps with position restraints and temperature coupling on. This is
followed by the full production run of 10ns with temperature and
pressure coupling turned off, H bonds are constrained using LINCS and a
time step of 1fs. For vacuum conditions, the periodic boundary
conditions are turned off, and no cut-offs are used. When I carry out
the 10ns simulation the total energy gradually increases, as does the
temperature from 300 to 500K. I presume this is because the temperature
coupling is turned off, however that is what I have noted from the
literature that others do for their vacuum simulations. Can anyone shed
any light on this? Following is my method.

integrator = md

tinit = 0

dt = 0.001

nsteps = 1000

nstxout = 2

nstvout = 2

nstfout = 0

nstlog = 10

nstenergy = 10

nstxtcout = 2

energygrps = Protein

nstcomm = 5

nstlist = 0

ns-type = simple

pbc = no

rlist = 0

coulombtype = Cut-off

rcoulomb = 0

epsilon_r = 2

vdw-type = Cut-off

rvdw =0

Tcoupl = no

tc-grps = Protein

tau_t = 0.1

ref_t = 300

Pcoupl = no

Pcoupltype = Isotropic

tau_p = 1

compressibility = 4.5e-5

ref_p = 1.0

gen_vel = yes ;

gen_temp = 300.0

gen_seed = -1

constraints = hbonds

constraint-algorithm = LINCS

lincs_order = 4

Thanks,

Zoe

Zoe Hall

Department of Chemistry

Oxford University

_zoe.h...@chem.ox.ac.uk_


Are you sure h-bonds are being constrained, because otherwise the time
step is too large? (maybe you need to write h-bonds). You may need to
increase the constraint accuracy as well. We did all our vacuum calcs in
double precision as well IIRC.







--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] Source Code for Lennard jones truncation schemes

[Apoorv Kalyankar]

Hello,

I was wondering where can I find the source code where the different
cut-off schemes (cut-off, shift, switch etc) for lennard jones
interactions have been implemented.
Thanks.

Apoorv
-- 
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Re: [gmx-users] Re: Simluations in vacuum - energy increase

[David van der Spoel]

On 2011-05-01 20.00, Zoe Hall wrote:

Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says 
"hbonds", not "h-bonds", however didn't make much difference which one I used. 
Could someone suggest the reason why you would want to turn temperature coupling off during the 
simulations - I don't really understand this.

In our work we want to study evaporation and cooling induced by the 
leaving water molecules. If you don't have water molecules, or even 
assume some kind of heat bath (e.g. a gas atmosphere), you could turn on 
T-coupling.

Thanks,

Zoe

On 2011-04-30 14.17, Zoe Hall wrote:

Gmx-users,

I am trying to carry out a simulation of lysozyme in vacuo using the
OPLS-AA forcefield. After energy minimisation, the protein is run for
10ps with position restraints and temperature coupling on. This is
followed by the full production run of 10ns with temperature and
pressure coupling turned off, H bonds are constrained using LINCS and a
time step of 1fs. For vacuum conditions, the periodic boundary
conditions are turned off, and no cut-offs are used. When I carry out
the 10ns simulation the total energy gradually increases, as does the
temperature from 300 to 500K. I presume this is because the temperature
coupling is turned off, however that is what I have noted from the
literature that others do for their vacuum simulations. Can anyone shed
any light on this? Following is my method.

integrator = md

tinit = 0

dt = 0.001

nsteps = 1000

nstxout = 2

nstvout = 2

nstfout = 0

nstlog = 10

nstenergy = 10

nstxtcout = 2

energygrps = Protein

nstcomm = 5

nstlist = 0

ns-type = simple

pbc = no

rlist = 0

coulombtype = Cut-off

rcoulomb = 0

epsilon_r = 2

vdw-type = Cut-off

rvdw =0

Tcoupl = no

tc-grps = Protein

tau_t = 0.1

ref_t = 300

Pcoupl = no

Pcoupltype = Isotropic

tau_p = 1

compressibility = 4.5e-5

ref_p = 1.0

gen_vel = yes ;

gen_temp = 300.0

gen_seed = -1

constraints = hbonds

constraint-algorithm = LINCS

lincs_order = 4

Thanks,

Zoe

Zoe Hall

Department of Chemistry

Oxford University

_zoe.h...@chem.ox.ac.uk_


Are you sure h-bonds are being constrained, because otherwise the time
step is too large? (maybe you need to write h-bonds). You may need to
increase the constraint accuracy as well. We did all our vacuum calcs in
double precision as well IIRC.




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Re: Simluations in vacuum - energy increase

[Zoe Hall]

Hi - thanks - much improved with shorter timestep and increase in constraint 
accuracy. Manual says "hbonds", not "h-bonds", however didn't make much 
difference which one I used. Could someone suggest the reason why you would 
want to turn temperature coupling off during the simulations - I don't really 
understand this. 

Thanks,

Zoe

On 2011-04-30 14.17, Zoe Hall wrote:
> Gmx-users,
>
> I am trying to carry out a simulation of lysozyme in vacuo using the
> OPLS-AA forcefield. After energy minimisation, the protein is run for
> 10ps with position restraints and temperature coupling on. This is
> followed by the full production run of 10ns with temperature and
> pressure coupling turned off, H bonds are constrained using LINCS and a
> time step of 1fs. For vacuum conditions, the periodic boundary
> conditions are turned off, and no cut-offs are used. When I carry out
> the 10ns simulation the total energy gradually increases, as does the
> temperature from 300 to 500K. I presume this is because the temperature
> coupling is turned off, however that is what I have noted from the
> literature that others do for their vacuum simulations. Can anyone shed
> any light on this? Following is my method.
>
> integrator = md
>
> tinit = 0
>
> dt = 0.001
>
> nsteps = 1000
>
> nstxout = 2
>
> nstvout = 2
>
> nstfout = 0
>
> nstlog = 10
>
> nstenergy = 10
>
> nstxtcout = 2
>
> energygrps = Protein
>
> nstcomm = 5
>
> nstlist = 0
>
> ns-type = simple
>
> pbc = no
>
> rlist = 0
>
> coulombtype = Cut-off
>
> rcoulomb = 0
>
> epsilon_r = 2
>
> vdw-type = Cut-off
>
> rvdw =0
>
> Tcoupl = no
>
> tc-grps = Protein
>
> tau_t = 0.1
>
> ref_t = 300
>
> Pcoupl = no
>
> Pcoupltype = Isotropic
>
> tau_p = 1
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> gen_vel = yes ;
>
> gen_temp = 300.0
>
> gen_seed = -1
>
> constraints = hbonds
>
> constraint-algorithm = LINCS
>
> lincs_order = 4
>
> Thanks,
>
> Zoe
>
> Zoe Hall
>
> Department of Chemistry
>
> Oxford University
>
> _zoe.h...@chem.ox.ac.uk_
>
Are you sure h-bonds are being constrained, because otherwise the time 
step is too large? (maybe you need to write h-bonds). You may need to 
increase the constraint accuracy as well. We did all our vacuum calcs in 
double precision as well IIRC.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se


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Re: [gmx-users] amber force field

[Justin A. Lemkul]

Maria Hamilton wrote:

Hi Justin

If I want to have Decane.itp file in Amber forcefield for TIP4P-EW what 
should I do?


In the future, please make sure to:

1. copy only the relevant portion of the digest
2. change the subject line to attract attention

To answer your question, the link I provided earlier contains all the relevant 
(general) points.  You'll have to derive parameters in some way consistent with 
the Amber force field of your choice (there are many parameter sets called 
"Amber").  Moreover, I already answered this question:


http://lists.gromacs.org/pipermail/gmx-users/2011-April/060897.html

-Justin



Thanks

Regards

Maria


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] lipid ff decisions

[chris . neale]

Has anybody done or read a good comparative study on what lipid ff  
works best in combination with proteins? There are so many options and  
I've realized that when anybody asks me what ff combination to use,  
all I can do is to tell them what combination I use and that so far it  
seems to work fine for me...


Thanks,
Chris.

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[gmx-users] Re: gmx-users Digest, Vol 85, Issue 2

[Maria Hamilton]

ou could take but I see this as the simplest
> solution.
>
> Cheers
>
> Tom
>
> Justin A. Lemkul wrote:
> >
> > Ioannis Beis wrote:
> >> Dear gromacs users,
> >>
> >> I am a new user of gromacs. I am currently trying to build a large
> >> bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and
> >> no protein embedded in it. I have used single lipids from
> >> pre-equilibrated bilayers available at Mr. Tieleman's website. The
> >> distance of center of mass of neighboring lipids is 1 nm, so there are
> >> small areas with overlaps. I was hoping that I would be able to inflate
> >> my membrane and have the lipids totally free of overlaps using
> >> Inflategro. Subsequently, I was planning to use the shrinking steps to
> >> bring the membrane into physiological size. Is this strategy valid in
> >> the first place? If not, I kindly ask for an alternative.
> >>
> >> In case this method can be used, despite "To identify the lipid species
> >> their actual residue name must be given" which is mentioned in the
> >> methodology, the form "INFLATEGRO bilayer.gro scaling_factor
> >> lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat
> >> (protein)" only allows the use of one lipid type. How is it possible to
> >> run perl with all lipid types at once? I have tried performing
> >> inflations using one lipid type at a time and they work. [It worths
> >> mentioning that the coordinates of the rest two (uninflated) lipid types
> >> slightly change without equilibration (I assume this has to do with
> >> Inflategro trying to force the molecules avoid overlaps)]. But I can't
> >> treat my membrane as a system that way. I have read the publication
> >> introducing the methodology, but it didn't help me solve my problem.
> >>
> >> I would be grateful if someone could help, also taking into account that
> >> I am
> >> inexperienced.
> >>
> >
> > If you want to use InflateGRO, then you'll have to modify the code to do
> so.  It
> > handles only one lipid type.
> >
> > The alternative is to use "normal" MD simulations to pack the membrane.
>  On such
> > approach (just thinking out loud here, so it may not work) might be to
> simulate
> > your membrane (maybe without water) with some external pressure applied
> to the
> > x-y plane to compress the lipids together.  You may need position
> restraints on,
> > i.e., the lipid headgroups in the z-dimension only during this procedure
> so the
> > lipids do not simply slam into one another and distort the membrane.
>  Once
> > you've achieved a reasonable membrane, solvate and equilibrate for a
> longer
> > period of time in the presence of solvent and absence of any restraints.
> >
> > -Justin
> >
> >> Kindest regards,
> >> Yiannis
> >>
> >
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
> --
>
> Message: 6
> Date: Sun, 1 May 2011 18:18:12 +0430 (IRDT)
> From: "Faezeh Kargar" 
> Subject: Re: [gmx-users] Fatal error: Attempting to read a checkpoint
>fileof version 12 with code of version 4
> To: "Discussion list for GROMACS users" 
> Message-ID: <28288.85.185.211.70.1304257692.squir...@mail.iasbs.ac.ir>
> Content-Type: text/plain; charset="utf-8"
>
>
> 
>
>
> Thank you very
> much for your reply. could you please tell me if there is any way to solve
> this problem and restart running the code?
> Karagr
>
> >
> On 30/04/2011 11:37 PM, Faezeh Kargar wrote:
> >>
> >>
> >> > On 4/30/2011 7:22 PM, Faezeh Kargar
> wrote:
> >> >>
> >> >> Dear gmx users,
> >> >>
> >> >> My code stops running because
> of electricity voltage oscillation. it
> >> >> happened for
> several times and each time I restarted running my code.
> >>
> >> but for this time with command
> >> >>
> >> >> mdrun -s topol.tpr -x
> >> >>
> traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt
> >> >> -e
> ener.part0002.part0003.part0004.part0004.part0005.edr -g
> >>
> >> md.part0002.part0003.part0004.part0004.part0005.log &
> >> >>
> >> >> I used this command before
> without any error. but now I encountered
> >> >> error

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

[Faezeh Kargar]

Thank you very
much for your reply. could you please tell me if there is any way to solve
this problem and restart running the code?
Karagr

>
On 30/04/2011 11:37 PM, Faezeh Kargar wrote:
>>
>>
>> > On 4/30/2011 7:22 PM, Faezeh Kargar
wrote:
>> >>
>> >> Dear gmx users,
>> >>
>> >> My code stops running because
of electricity voltage oscillation. it
>> >> happened for
several times and each time I restarted running my code.
>>
>> but for this time with command
>> >>
>> >> mdrun -s topol.tpr -x
>> >>
traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt
>> >> -e
ener.part0002.part0003.part0004.part0004.part0005.edr -g
>>
>> md.part0002.part0003.part0004.part0004.part0005.log &
>> >>
>> >> I used this command before
without any error. but now I encountered
>> >> error like
this:
>> >>
>> >>
>> >>
Program mdrun, VERSION 4.0.7
>> >> Source
>>
>> code file: checkpoint.c, line: 565
>> >>
>> >> Fatal error:
>> >> Attempting
>> >> to read a checkpoint file of version 12 with code of
version 4
>> >>
>> >> I looked at the
file "checkpoint.c". at first the version of
>>
>> checkpoint file is 4 but I do not know how and why it changes.
>> >>
>> >
>> > The usual reason
for this kind of error is that you're using an old
>> >
version of GROMACS to access a file written by a new version. That's
>> not
>> > a good idea.
>> >
>> > Mark
>> >
>>
>> Thank
you for your reply. I just use version 4.0.7 of GROMACS and all
>> of files are written by this version. as I said before, I
could
>> restart running of my codes with this command without
any problem.
>>
> 
> Version 12 is that used in
4.5.x, so I think you are using that version.
> Someone may have
changed the software and not told you about it (in
> which case,
tell them to stop wasting people's time). Or you've migrated
>
files from one place to another, or something similar.
> 
> Mark
> --
> gmx-users mailing list   
gmx-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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> 
> --
> This message has been scanned for viruses
and
> dangerous content by MailScanner, and is
> believed
to be clean.
> 
> 


-- 
83_kargar

-- 
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Re: [gmx-users] How to use Inflategro with different lipid types

[Thomas Piggot]

Hi,

To construct the bilayer I would just take an equilibrated POPC bilayer 
and then randomly pick lipids to change to POPE (just by a simple 
renaming of these lipids and the atom names in the headgroup) and DPPC 
(which would just require deletion of two united-atoms from the sn-2 
chains and renaming of the lipids). Then just run for an equilibration 
on the bilayer to allow the changes to take effect.


There are other approaches you could take but I see this as the simplest 
solution.


Cheers

Tom

Justin A. Lemkul wrote:


Ioannis Beis wrote:

Dear gromacs users,

I am a new user of gromacs. I am currently trying to build a large 
bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and 
no protein embedded in it. I have used single lipids from 
pre-equilibrated bilayers available at Mr. Tieleman's website. The 
distance of center of mass of neighboring lipids is 1 nm, so there are 
small areas with overlaps. I was hoping that I would be able to inflate 
my membrane and have the lipids totally free of overlaps using 
Inflategro. Subsequently, I was planning to use the shrinking steps to 
bring the membrane into physiological size. Is this strategy valid in 
the first place? If not, I kindly ask for an alternative.


In case this method can be used, despite "To identify the lipid species 
their actual residue name must be given" which is mentioned in the 
methodology, the form "INFLATEGRO bilayer.gro scaling_factor 
lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat 
(protein)" only allows the use of one lipid type. How is it possible to 
run perl with all lipid types at once? I have tried performing 
inflations using one lipid type at a time and they work. [It worths 
mentioning that the coordinates of the rest two (uninflated) lipid types 
slightly change without equilibration (I assume this has to do with 
Inflategro trying to force the molecules avoid overlaps)]. But I can't 
treat my membrane as a system that way. I have read the publication 
introducing the methodology, but it didn't help me solve my problem.


I would be grateful if someone could help, also taking into account that 
I am

inexperienced.



If you want to use InflateGRO, then you'll have to modify the code to do so.  It 
handles only one lipid type.


The alternative is to use "normal" MD simulations to pack the membrane.  On such 
approach (just thinking out loud here, so it may not work) might be to simulate 
your membrane (maybe without water) with some external pressure applied to the 
x-y plane to compress the lipids together.  You may need position restraints on, 
i.e., the lipid headgroups in the z-dimension only during this procedure so the 
lipids do not simply slam into one another and distort the membrane.  Once 
you've achieved a reasonable membrane, solvate and equilibrate for a longer 
period of time in the presence of solvent and absence of any restraints.


-Justin


Kindest regards,
Yiannis





--
Dr Thomas Piggot
University of Southampton, UK.
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Re: [gmx-users] How to use Inflategro with different lipid types

[Justin A. Lemkul]

Ioannis Beis wrote:

Dear gromacs users,

I am a new user of gromacs. I am currently trying to build a large 
bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and 
no protein embedded in it. I have used single lipids from 
pre-equilibrated bilayers available at Mr. Tieleman's website. The 
distance of center of mass of neighboring lipids is 1 nm, so there are 
small areas with overlaps. I was hoping that I would be able to inflate 
my membrane and have the lipids totally free of overlaps using 
Inflategro. Subsequently, I was planning to use the shrinking steps to 
bring the membrane into physiological size. Is this strategy valid in 
the first place? If not, I kindly ask for an alternative.


In case this method can be used, despite "To identify the lipid species 
their actual residue name must be given" which is mentioned in the 
methodology, the form "INFLATEGRO bilayer.gro scaling_factor 
lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat 
(protein)" only allows the use of one lipid type. How is it possible to 
run perl with all lipid types at once? I have tried performing 
inflations using one lipid type at a time and they work. [It worths 
mentioning that the coordinates of the rest two (uninflated) lipid types 
slightly change without equilibration (I assume this has to do with 
Inflategro trying to force the molecules avoid overlaps)]. But I can't 
treat my membrane as a system that way. I have read the publication 
introducing the methodology, but it didn't help me solve my problem.


I would be grateful if someone could help, also taking into account that 
I am

inexperienced.



If you want to use InflateGRO, then you'll have to modify the code to do so.  It 
handles only one lipid type.


The alternative is to use "normal" MD simulations to pack the membrane.  On such 
approach (just thinking out loud here, so it may not work) might be to simulate 
your membrane (maybe without water) with some external pressure applied to the 
x-y plane to compress the lipids together.  You may need position restraints on, 
i.e., the lipid headgroups in the z-dimension only during this procedure so the 
lipids do not simply slam into one another and distort the membrane.  Once 
you've achieved a reasonable membrane, solvate and equilibrate for a longer 
period of time in the presence of solvent and absence of any restraints.


-Justin


Kindest regards,
Yiannis



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] reg error in coordinate file

[Justin A. Lemkul]

vidhya sankar wrote:

Dear gmx-user,
   when i run Equilibration Phase (nvt.mdp) i got 
the .gro files as follows

that is co-ordinates not defined in my .gro file
 What should i change in my mdp file in order to remove 'nan' and to 
obtain coordinate?


I doubt the problem is that simple.  "Nan" means "not a number," and thus 
represents some infinite value.  So either:


1. your system blew up at the last step when the .gro file was written
2. there is some bug that needs to be fixed
3. your file system had some problem writing the .gro file

To address (1), check the .log file for any pertinent messages about 
instability.  For (2), you'll have to at least provide your Gromacs version, 
input settings (.mdp file), and perhaps a description of the hardware.  For (3), 
check your output trajectory with gmxcheck and/or watch it in VMD (or your 
favorite viewer) and if its contents are normal and the .gro file is the only 
aberrant output, then it's your file system's fault, no Gromacs'.





   6.56000   4.36200  12.0


For a system of just 80 atoms, this box seems extraordinarily large.  Quite 
likely your system blew up.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] amber force field

[Justin A. Lemkul]

Maria Hamilton wrote:

Hi all friends

If I want to use tip4pew model for water from Amber forcefield, can I 
use itp files in PRODRG site for the other components?




PRODRG topologies are (supposedly) compatible with Gromos force fields, but 
TIP4P-EW is not implemented for any of these parameter sets.  Any attempt to 
combine these would inevitably result in fatal errors from grompp about missing 
atomtypes.  More to the point, one should never mix and match force fields. 
See, for instance, the discussion at:


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin


Thanks

Regards

Maria



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] amber force field

[lina]

In latest version of gromacs (4.5.4 or earlier)

The amber force fields were provided.


-- 
Best Regards,

lina
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[gmx-users] reg error in coordinate file

[vidhya sankar]

Dear gmx-user, 
   when i run Equilibration Phase (nvt.mdp) i got the .gro 
files as follows 
that is co-ordinates not defined in my .gro file
 What should i change in my mdp file in order to remove 'nan' and to obtain 
coordinate?
HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
   80
    1HEM FE    1 nan nan nan nan nan nan
    1HEM NA    2 nan nan nan nan nan nan
    1HEM NB    3 nan nan nan nan nan nan
    1HEM NC    4 nan nan nan nan nan nan
    1HEM ND    5 nan nan nan nan nan nan
    1HEM    CHA    6 nan nan nan nan nan nan
    1HEM    HHA    7 nan nan nan nan nan nan
    1HEM    C1A    8 nan nan nan nan nan nan
    1HEM    C2A    9 nan nan nan nan nan nan
    1HEM    C3A   10 nan nan nan nan nan nan
    1HEM    C4A   11 nan nan nan nan nan nan
    1HEM    CMA   12 nan nan nan nan nan nan
    1HEM    CAA   13 nan nan nan nan nan nan
    1HEM    CBA   14 nan nan nan nan nan nan
    1HEM    CGA   15 nan nan nan nan nan nan
    1HEM    O1A   16 nan nan nan nan nan nan
    1HEM    O2A   17 nan nan nan nan nan nan
    1HEM    CHB   18 nan nan nan nan nan nan
    1HEM    HHB   19 nan nan nan nan nan nan
    1HEM    C1B   20 nan nan nan nan nan nan
    1HEM    C2B   21 nan nan nan nan nan nan
    1HEM    C3B   22 nan nan nan nan nan nan
    1HEM    C4B   23 nan nan nan nan nan nan
    1HEM    CMB   24 nan nan nan nan nan nan
    1HEM    CAB   25 nan nan nan nan nan nan
    1HEM    CBB   26 nan nan nan nan nan nan
    1HEM    CHC   27 nan nan nan nan nan nan
    1HEM    HHC   28 nan nan nan nan nan nan
    1HEM    C1C   29 nan nan nan nan nan nan
    1HEM    C2C   30 nan nan nan nan nan nan
    1HEM    C3C   31 nan nan nan nan nan nan
    1HEM    C4C   32 nan nan nan nan nan nan
    1HEM    CMC   33 nan nan nan nan nan nan
    1HEM    CAC   34 nan nan nan nan nan nan
    1HEM    CBC   35 nan nan nan nan nan nan
    1HEM    CHD   36 nan nan nan nan nan nan
    1HEM    HHD   37 nan nan nan nan nan nan
    1HEM    C1D   38 nan nan nan nan nan nan
    1HEM    C2D   39 nan nan nan nan nan nan
    1HEM    C3D   40 nan nan nan nan nan nan
    1HEM    C4D   41 nan nan nan nan nan nan
    1HEM    CMD   42 nan nan nan nan nan nan
    1HEM    CAD   43 nan nan nan nan nan nan
    1HEM    CBD   44 nan nan nan nan nan nan
    1HEM    CGD   45 nan nan nan nan nan nan
    1HEM    O1D   46 nan nan nan nan nan nan
    1HEM    O2D   47 nan nan nan nan nan nan
    2OXY O1   48 nan nan nan nan nan nan
    2OXY O2   49 nan nan nan nan nan nan
    3SOL OW   50 nan nan nan nan nan nan
    3SOL    HW1   51 nan nan nan nan nan nan
    3SOL    HW2   52 nan nan nan nan nan nan
    4SOL OW   53 nan nan nan nan nan nan
    4SOL    HW1   54 nan nan nan nan nan nan
    4SOL    HW2   55 nan nan nan nan nan nan
    5SOL OW   56 nan nan nan nan nan nan
    5SOL    HW1   57 nan nan nan nan nan nan
    5SOL    HW2   58 nan nan nan nan nan nan
    6SOL OW   59 nan nan nan nan nan nan
    6SOL    HW1   60 nan nan nan nan nan nan
    6SOL    HW2   61 nan nan nan nan nan nan
    7SOL OW   62 nan nan nan nan nan nan
    7SOL    HW1   63 nan nan nan nan nan nan
    7SOL    HW2   64 nan nan nan nan nan nan
    8SOL OW   65 nan nan nan nan nan nan
    8SOL    HW1   66 nan nan nan nan nan nan
    8SOL    HW2   67 nan nan nan nan nan nan
    9SOL OW   68 nan nan nan nan nan nan
    9SOL    HW1 

[gmx-users] amber force field

[Maria Hamilton]

Hi all friends

If I want to use tip4pew model for water from Amber forcefield, can I use
itp files in PRODRG site for the other components?

Thanks

Regards

Maria
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