Re: [gmx-users] I want to drag two atoms together with GROMCS SMD options.

[Vytautas Rakeviius]

Thanks, and now after some time I get:"Pull reference distance for coordinate 3 
() needs to be non-negative"How to solve this error?
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Re: [gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

Is the modified parameter file for POPG from your work available online?

Merril.

On 10 Mar 2017 7:05 a.m., "Merril Mathew"  wrote:

> many thanks Tom.
>
> On 10 Mar 2017 1:35 a.m., "Thomas Piggot"  wrote:
>
>> So this isn't a berger based PG rather a pure GROMOS one. But yes, it
>> also has problems. The double bond dihedrals don't work well and so you get
>> really poor order parameters after the double bond (see
>> http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is
>> true of POPG). From what I remember, this itp also has extraneous dihedrals
>> in the glycerol regions plus some other issues with the bonded parameters (
>> http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I cannot remember
>> off the top of my head the impact they made.
>>
>> Up to you to decide with the density calculation.
>>
>> Cheers
>>
>> Tom
>>
>> On 10/03/17 00:45, Merril Mathew wrote:
>>
>>> The POPG .itp and .pdb files were obtained from,
>>> https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
>>> Author : A Kukol.
>>>   I used D-POPG. Should I use electron density or mass for calculating
>>> monolayer thickness?
>>>
>>> Merril.
>>>
>>> On 10 Mar 2017 00:36, "Thomas Piggot"  wrote:
>>>
>>> How did you get/make the itp for POPG, this isn't available from the
 Tieleman group website. The Berger parameters don't work well for PG.
 For
 example, you will see ring like structures in the head group if you
 look at
 the simulations in something like VMD. The APL for bilayers (and I
 imagine
 monolayers) will also be too low. You can find more details in
 http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore
 models
 are Berger based ones).

 For the APL, the calculation is trivial using the box vectors (from gmx
 energy or gmx traj). For the thickness, you can probably use gmx
 density to
 create a density profile of your monolayer and work out a thickness from
 that.

 Tom

 On 10/03/17 00:24, Merril Mathew wrote:

 I am using Berger lipid from Dr.Tielemens website and modified the
> gromos
> forcefield to include the lipid parameters. Out of interest, Do you
> know
> any gromacs tools or other programs that calculatg the area per lipid
> and
> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
> but
> it only works with bilyer lipids. thanks.
>
> Merril.
>
> On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:
>
> Sort of. The saturated carbons after the double bond will be correct
> too,
>
>> just not C9 and C10 in the double bond (as you need different
>> assumptions
>> for calculating these in united-atom system which the -unsat option is
>> meant to do correctly but doesn't). Additionally, there are tools out
>> there
>> that will work for calculating the order parameters of the unsaturated
>> bond
>> if you need it.
>>
>> GROMOS 53A6 is not really a lipid force field per say but there are PG
>> compatible lipids (Kukol, different Berger variants, GROMOS-CKP).
>> Which
>> lipid parameters are you using? Lots of them don't work well at all.
>>
>> Cheers
>>
>> Tom
>>
>> On 10/03/17 00:10, Merril Mathew wrote:
>>
>> Hi,
>>
>>> I am using a united atom forcefield. gromos53a6. So does that mean as
>>> long
>>> as I avoid the double bond and the subsequent carbons after the
>>> double
>>> bond, then the calculation is correct?  I understand it does not
>>> describe
>>> the full lipid length but can be used to assess the monolayer
>>> behaviour
>>> roughly.
>>>
>>> Merril.
>>>
>>> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" 
>>> wrote:
>>>
>>> The order parameters calculated for all the saturated carbons will be
>>>
>>> correct but the gmx order program doesn't calculate the order
 parameters
 for the unsaturated carbons correctly (even when using the -unsat
 option).

 Out of interest, is this a united-atom or all-atom force field you
 are
 using?

 Cheers

 Tom

 On 09/03/17 23:51, Merril Mathew wrote:

 Hi,

 I followed turorials found on Bevanlab by Justin. I successfully
> calculated
> order parameter for DPPC molecules in my system following the
> tutorial.
> My
> question is whether the same calculation can be applied for a POPG
> molecule
> with a double bond in the acyl chain.? can I group all the carbon
> upto
> the
> double bond, therefore ignoring the double bond and the rest of the
> carbons
> in the chain to calculate 

Re: [gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

many thanks Tom.

On 10 Mar 2017 1:35 a.m., "Thomas Piggot"  wrote:

> So this isn't a berger based PG rather a pure GROMOS one. But yes, it also
> has problems. The double bond dihedrals don't work well and so you get
> really poor order parameters after the double bond (see
> http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is
> true of POPG). From what I remember, this itp also has extraneous dihedrals
> in the glycerol regions plus some other issues with the bonded parameters (
> http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I cannot remember
> off the top of my head the impact they made.
>
> Up to you to decide with the density calculation.
>
> Cheers
>
> Tom
>
> On 10/03/17 00:45, Merril Mathew wrote:
>
>> The POPG .itp and .pdb files were obtained from,
>> https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
>> Author : A Kukol.
>>   I used D-POPG. Should I use electron density or mass for calculating
>> monolayer thickness?
>>
>> Merril.
>>
>> On 10 Mar 2017 00:36, "Thomas Piggot"  wrote:
>>
>> How did you get/make the itp for POPG, this isn't available from the
>>> Tieleman group website. The Berger parameters don't work well for PG. For
>>> example, you will see ring like structures in the head group if you look
>>> at
>>> the simulations in something like VMD. The APL for bilayers (and I
>>> imagine
>>> monolayers) will also be too low. You can find more details in
>>> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore
>>> models
>>> are Berger based ones).
>>>
>>> For the APL, the calculation is trivial using the box vectors (from gmx
>>> energy or gmx traj). For the thickness, you can probably use gmx density
>>> to
>>> create a density profile of your monolayer and work out a thickness from
>>> that.
>>>
>>> Tom
>>>
>>> On 10/03/17 00:24, Merril Mathew wrote:
>>>
>>> I am using Berger lipid from Dr.Tielemens website and modified the gromos
 forcefield to include the lipid parameters. Out of interest, Do you know
 any gromacs tools or other programs that calculatg the area per lipid
 and
 bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
 but
 it only works with bilyer lipids. thanks.

 Merril.

 On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:

 Sort of. The saturated carbons after the double bond will be correct
 too,

> just not C9 and C10 in the double bond (as you need different
> assumptions
> for calculating these in united-atom system which the -unsat option is
> meant to do correctly but doesn't). Additionally, there are tools out
> there
> that will work for calculating the order parameters of the unsaturated
> bond
> if you need it.
>
> GROMOS 53A6 is not really a lipid force field per say but there are PG
> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
> lipid parameters are you using? Lots of them don't work well at all.
>
> Cheers
>
> Tom
>
> On 10/03/17 00:10, Merril Mathew wrote:
>
> Hi,
>
>> I am using a united atom forcefield. gromos53a6. So does that mean as
>> long
>> as I avoid the double bond and the subsequent carbons after the double
>> bond, then the calculation is correct?  I understand it does not
>> describe
>> the full lipid length but can be used to assess the monolayer
>> behaviour
>> roughly.
>>
>> Merril.
>>
>> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" 
>> wrote:
>>
>> The order parameters calculated for all the saturated carbons will be
>>
>> correct but the gmx order program doesn't calculate the order
>>> parameters
>>> for the unsaturated carbons correctly (even when using the -unsat
>>> option).
>>>
>>> Out of interest, is this a united-atom or all-atom force field you
>>> are
>>> using?
>>>
>>> Cheers
>>>
>>> Tom
>>>
>>> On 09/03/17 23:51, Merril Mathew wrote:
>>>
>>> Hi,
>>>
>>> I followed turorials found on Bevanlab by Justin. I successfully
 calculated
 order parameter for DPPC molecules in my system following the
 tutorial.
 My
 question is whether the same calculation can be applied for a POPG
 molecule
 with a double bond in the acyl chain.? can I group all the carbon
 upto
 the
 double bond, therefore ignoring the double bond and the rest of the
 carbons
 in the chain to calculate order parameter? Is that a reasonable
 analysis
 to
 measure the order of POPG molecules.? Thanks.

 --

 Dr Thomas Piggot
>>> Visiting Fellow
>>> University of Southampton, UK.
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the 

[gmx-users] g_energy for comparing total energies of 2 similar systems

[#SUKRITI GUPTA#]

Dear all,


I have two systems: 1. metal ion in water with a counter ion present in the 
bulk & 2. Exactly same system (with same no. of atoms as the previous one) with 
counter ion present in metal's first solvation shell.


Will it be fair to compare the total energies of both the systems obtained 
after production run using g_energy? Can we say the one with higher negative 
values is the more stable state?

Also, is it better to compare energies obtained using g_energy without any 
extra flag or the estimated free energy using the flag -fee in the g_energy 
command?


Regards


Sukriti

[https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.]

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | 
Web:erian.ntu.edu.sg



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Re: [gmx-users] Order parameter for double bonded lipids

[Thomas Piggot]

So this isn't a berger based PG rather a pure GROMOS one. But yes, it 
also has problems. The double bond dihedrals don't work well and so you 
get really poor order parameters after the double bond (see 
http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is 
true of POPG). From what I remember, this itp also has extraneous 
dihedrals in the glycerol regions plus some other issues with the bonded 
parameters (http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I 
cannot remember off the top of my head the impact they made.


Up to you to decide with the density calculation.

Cheers

Tom

On 10/03/17 00:45, Merril Mathew wrote:

The POPG .itp and .pdb files were obtained from,
https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
Author : A Kukol.
  I used D-POPG. Should I use electron density or mass for calculating
monolayer thickness?

Merril.

On 10 Mar 2017 00:36, "Thomas Piggot"  wrote:


How did you get/make the itp for POPG, this isn't available from the
Tieleman group website. The Berger parameters don't work well for PG. For
example, you will see ring like structures in the head group if you look at
the simulations in something like VMD. The APL for bilayers (and I imagine
monolayers) will also be too low. You can find more details in
http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore models
are Berger based ones).

For the APL, the calculation is trivial using the box vectors (from gmx
energy or gmx traj). For the thickness, you can probably use gmx density to
create a density profile of your monolayer and work out a thickness from
that.

Tom

On 10/03/17 00:24, Merril Mathew wrote:


I am using Berger lipid from Dr.Tielemens website and modified the gromos
forcefield to include the lipid parameters. Out of interest, Do you know
any gromacs tools or other programs that calculatg the area per lipid and
bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
but
it only works with bilyer lipids. thanks.

Merril.

On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:

Sort of. The saturated carbons after the double bond will be correct too,

just not C9 and C10 in the double bond (as you need different assumptions
for calculating these in united-atom system which the -unsat option is
meant to do correctly but doesn't). Additionally, there are tools out
there
that will work for calculating the order parameters of the unsaturated
bond
if you need it.

GROMOS 53A6 is not really a lipid force field per say but there are PG
compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
lipid parameters are you using? Lots of them don't work well at all.

Cheers

Tom

On 10/03/17 00:10, Merril Mathew wrote:

Hi,

I am using a united atom forcefield. gromos53a6. So does that mean as
long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct?  I understand it does not
describe
the full lipid length but can be used to assess the monolayer behaviour
roughly.

Merril.

On 10 Mar 2017 12:04 a.m., "Thomas Piggot" 
wrote:

The order parameters calculated for all the saturated carbons will be


correct but the gmx order program doesn't calculate the order
parameters
for the unsaturated carbons correctly (even when using the -unsat
option).

Out of interest, is this a united-atom or all-atom force field you are
using?

Cheers

Tom

On 09/03/17 23:51, Merril Mathew wrote:

Hi,


I followed turorials found on Bevanlab by Justin. I successfully
calculated
order parameter for DPPC molecules in my system following the
tutorial.
My
question is whether the same calculation can be applied for a POPG
molecule
with a double bond in the acyl chain.? can I group all the carbon upto
the
double bond, therefore ignoring the double bond and the rest of the
carbons
in the chain to calculate order parameter? Is that a reasonable
analysis
to
measure the order of POPG molecules.? Thanks.

--


Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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--

Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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Re: [gmx-users] Calculating area per lipid and monolayer thickness

[Merril Mathew]

thanks Justin.

On 8 Mar 2017 13:09, "Justin Lemkul"  wrote:

>
>
> On 3/8/17 8:06 AM, Merril Mathew wrote:
>
>> I dont know what I am doing wrong. There is no Box-X or Box-Y when
>> prompted. These are the list I get:
>> -
>>   1  Angle2  Proper-Dih.  3  Ryckaert-Bell.   4
>> Improper-Dih.
>>   5  LJ-146  Coulomb-14   7  LJ-(SR)  8
>> Disper.-corr.
>>   9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
>> Kinetic-En.
>>  13  Total-Energy14  Conserved-En.   15  Temperature 16
>> Pres.-DC
>>  17  Pressure18  Constr.-rmsd19  Vir-XX  20
>> Vir-XY
>>  21  Vir-XZ  22  Vir-YX  23  Vir-YY  24
>> Vir-YZ
>>  25  Vir-ZX  26  Vir-ZY  27  Vir-ZZ  28
>> Pres-XX
>>  29  Pres-XY 30  Pres-XZ 31  Pres-YX 32
>> Pres-YY
>>  33  Pres-YZ 34  Pres-ZX 35  Pres-ZY 36
>> Pres-ZZ
>>  37  #Surf*SurfTen   38  T-DPOPG_OPO 39  T-SOL_Ion
>>
>> 38 and 39 are the coupling groups I used.
>>
>
> If there is no option to select box vectors, then your simulation was NVT
> and by definition the box vectors don't vary and your membrane area is
> constant.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] Use of -nr for order parameters

[Justin Lemkul]

On 3/9/17 2:41 PM, Wally Davis wrote:

My input line is:
gmx order -s test.tpr -f fullTraj.trr -n orderParam.ndx
The index file is formated with 3 groups, one per carbon along the chain of 
interest.
The error I get is: "In option nr  Required option was not provided, and the default 
file 'index' does not exist or is not accessible.   The following extensions were tried 
to complete the file name:  .ndx"
Every example I have seen online does not include an nr option. Any ideas on 
what this is or how to get rid of the error?



The index file passed to -nr is only for radial axis calculations, invoked via 
the -radial option.  This shouldn't be possible with the command given above.


-Justin


On Wednesday, March 8, 2017 5:31 PM, Justin Lemkul  wrote:




On 3/8/17 4:46 PM, Wally Davis wrote:

Hi,
I'm trying to use the g_order function. I have formated my .ndx file with one 
group per carbon and provide this file under the -n input option. However, I 
alway get the error that the -nr file is not found. What is the extra .ndx file 
I need to provide?



Please provide your full command and all relevant screen output, including the
error.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

I also used the same POPG .itp and .pdb files to edit and create an
oxidised version of the molecule with aldehyde group replacing the double
bond. Is there a problem associated with parameters from A Kukol for POPG?

On 10 Mar 2017 00:45, "Merril Mathew"  wrote:

> The POPG .itp and .pdb files were obtained from,
> https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
> Author : A Kukol.
>  I used D-POPG. Should I use electron density or mass for calculating
> monolayer thickness?
>
> Merril.
>
> On 10 Mar 2017 00:36, "Thomas Piggot"  wrote:
>
>> How did you get/make the itp for POPG, this isn't available from the
>> Tieleman group website. The Berger parameters don't work well for PG. For
>> example, you will see ring like structures in the head group if you look at
>> the simulations in something like VMD. The APL for bilayers (and I imagine
>> monolayers) will also be too low. You can find more details in
>> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore
>> models are Berger based ones).
>>
>> For the APL, the calculation is trivial using the box vectors (from gmx
>> energy or gmx traj). For the thickness, you can probably use gmx density to
>> create a density profile of your monolayer and work out a thickness from
>> that.
>>
>> Tom
>>
>> On 10/03/17 00:24, Merril Mathew wrote:
>>
>>> I am using Berger lipid from Dr.Tielemens website and modified the gromos
>>> forcefield to include the lipid parameters. Out of interest, Do you know
>>> any gromacs tools or other programs that calculatg the area per lipid and
>>> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
>>> but
>>> it only works with bilyer lipids. thanks.
>>>
>>> Merril.
>>>
>>> On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:
>>>
>>> Sort of. The saturated carbons after the double bond will be correct too,
 just not C9 and C10 in the double bond (as you need different
 assumptions
 for calculating these in united-atom system which the -unsat option is
 meant to do correctly but doesn't). Additionally, there are tools out
 there
 that will work for calculating the order parameters of the unsaturated
 bond
 if you need it.

 GROMOS 53A6 is not really a lipid force field per say but there are PG
 compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
 lipid parameters are you using? Lots of them don't work well at all.

 Cheers

 Tom

 On 10/03/17 00:10, Merril Mathew wrote:

 Hi,
>
> I am using a united atom forcefield. gromos53a6. So does that mean as
> long
> as I avoid the double bond and the subsequent carbons after the double
> bond, then the calculation is correct?  I understand it does not
> describe
> the full lipid length but can be used to assess the monolayer behaviour
> roughly.
>
> Merril.
>
> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" 
> wrote:
>
> The order parameters calculated for all the saturated carbons will be
>
>> correct but the gmx order program doesn't calculate the order
>> parameters
>> for the unsaturated carbons correctly (even when using the -unsat
>> option).
>>
>> Out of interest, is this a united-atom or all-atom force field you are
>> using?
>>
>> Cheers
>>
>> Tom
>>
>> On 09/03/17 23:51, Merril Mathew wrote:
>>
>> Hi,
>>
>>> I followed turorials found on Bevanlab by Justin. I successfully
>>> calculated
>>> order parameter for DPPC molecules in my system following the
>>> tutorial.
>>> My
>>> question is whether the same calculation can be applied for a POPG
>>> molecule
>>> with a double bond in the acyl chain.? can I group all the carbon
>>> upto
>>> the
>>> double bond, therefore ignoring the double bond and the rest of the
>>> carbons
>>> in the chain to calculate order parameter? Is that a reasonable
>>> analysis
>>> to
>>> measure the order of POPG molecules.? Thanks.
>>>
>>> --
>>>
>> Dr Thomas Piggot
>> Visiting Fellow
>> University of Southampton, UK.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>> --
 Dr Thomas Piggot
 Visiting Fellow
 University of Southampton, UK.

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Re: [gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

The POPG .itp and .pdb files were obtained from,
https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
Author : A Kukol.
 I used D-POPG. Should I use electron density or mass for calculating
monolayer thickness?

Merril.

On 10 Mar 2017 00:36, "Thomas Piggot"  wrote:

> How did you get/make the itp for POPG, this isn't available from the
> Tieleman group website. The Berger parameters don't work well for PG. For
> example, you will see ring like structures in the head group if you look at
> the simulations in something like VMD. The APL for bilayers (and I imagine
> monolayers) will also be too low. You can find more details in
> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore models
> are Berger based ones).
>
> For the APL, the calculation is trivial using the box vectors (from gmx
> energy or gmx traj). For the thickness, you can probably use gmx density to
> create a density profile of your monolayer and work out a thickness from
> that.
>
> Tom
>
> On 10/03/17 00:24, Merril Mathew wrote:
>
>> I am using Berger lipid from Dr.Tielemens website and modified the gromos
>> forcefield to include the lipid parameters. Out of interest, Do you know
>> any gromacs tools or other programs that calculatg the area per lipid and
>> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
>> but
>> it only works with bilyer lipids. thanks.
>>
>> Merril.
>>
>> On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:
>>
>> Sort of. The saturated carbons after the double bond will be correct too,
>>> just not C9 and C10 in the double bond (as you need different assumptions
>>> for calculating these in united-atom system which the -unsat option is
>>> meant to do correctly but doesn't). Additionally, there are tools out
>>> there
>>> that will work for calculating the order parameters of the unsaturated
>>> bond
>>> if you need it.
>>>
>>> GROMOS 53A6 is not really a lipid force field per say but there are PG
>>> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
>>> lipid parameters are you using? Lots of them don't work well at all.
>>>
>>> Cheers
>>>
>>> Tom
>>>
>>> On 10/03/17 00:10, Merril Mathew wrote:
>>>
>>> Hi,

 I am using a united atom forcefield. gromos53a6. So does that mean as
 long
 as I avoid the double bond and the subsequent carbons after the double
 bond, then the calculation is correct?  I understand it does not
 describe
 the full lipid length but can be used to assess the monolayer behaviour
 roughly.

 Merril.

 On 10 Mar 2017 12:04 a.m., "Thomas Piggot" 
 wrote:

 The order parameters calculated for all the saturated carbons will be

> correct but the gmx order program doesn't calculate the order
> parameters
> for the unsaturated carbons correctly (even when using the -unsat
> option).
>
> Out of interest, is this a united-atom or all-atom force field you are
> using?
>
> Cheers
>
> Tom
>
> On 09/03/17 23:51, Merril Mathew wrote:
>
> Hi,
>
>> I followed turorials found on Bevanlab by Justin. I successfully
>> calculated
>> order parameter for DPPC molecules in my system following the
>> tutorial.
>> My
>> question is whether the same calculation can be applied for a POPG
>> molecule
>> with a double bond in the acyl chain.? can I group all the carbon upto
>> the
>> double bond, therefore ignoring the double bond and the rest of the
>> carbons
>> in the chain to calculate order parameter? Is that a reasonable
>> analysis
>> to
>> measure the order of POPG molecules.? Thanks.
>>
>> --
>>
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>>> Dr Thomas Piggot
>>> Visiting Fellow
>>> University of Southampton, UK.
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
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>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List 

Re: [gmx-users] Order parameter for double bonded lipids

[Thomas Piggot]

How did you get/make the itp for POPG, this isn't available from the 
Tieleman group website. The Berger parameters don't work well for PG. 
For example, you will see ring like structures in the head group if you 
look at the simulations in something like VMD. The APL for bilayers (and 
I imagine monolayers) will also be too low. You can find more details in 
http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore 
models are Berger based ones).


For the APL, the calculation is trivial using the box vectors (from gmx 
energy or gmx traj). For the thickness, you can probably use gmx density 
to create a density profile of your monolayer and work out a thickness 
from that.


Tom

On 10/03/17 00:24, Merril Mathew wrote:

I am using Berger lipid from Dr.Tielemens website and modified the gromos
forcefield to include the lipid parameters. Out of interest, Do you know
any gromacs tools or other programs that calculatg the area per lipid and
bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM but
it only works with bilyer lipids. thanks.

Merril.

On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:


Sort of. The saturated carbons after the double bond will be correct too,
just not C9 and C10 in the double bond (as you need different assumptions
for calculating these in united-atom system which the -unsat option is
meant to do correctly but doesn't). Additionally, there are tools out there
that will work for calculating the order parameters of the unsaturated bond
if you need it.

GROMOS 53A6 is not really a lipid force field per say but there are PG
compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
lipid parameters are you using? Lots of them don't work well at all.

Cheers

Tom

On 10/03/17 00:10, Merril Mathew wrote:


Hi,

I am using a united atom forcefield. gromos53a6. So does that mean as long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct?  I understand it does not describe
the full lipid length but can be used to assess the monolayer behaviour
roughly.

Merril.

On 10 Mar 2017 12:04 a.m., "Thomas Piggot"  wrote:

The order parameters calculated for all the saturated carbons will be

correct but the gmx order program doesn't calculate the order parameters
for the unsaturated carbons correctly (even when using the -unsat
option).

Out of interest, is this a united-atom or all-atom force field you are
using?

Cheers

Tom

On 09/03/17 23:51, Merril Mathew wrote:

Hi,

I followed turorials found on Bevanlab by Justin. I successfully
calculated
order parameter for DPPC molecules in my system following the tutorial.
My
question is whether the same calculation can be applied for a POPG
molecule
with a double bond in the acyl chain.? can I group all the carbon upto
the
double bond, therefore ignoring the double bond and the rest of the
carbons
in the chain to calculate order parameter? Is that a reasonable analysis
to
measure the order of POPG molecules.? Thanks.

--

Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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--
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University of Southampton, UK.

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University of Southampton, UK.

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Re: [gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

I am using Berger lipid from Dr.Tielemens website and modified the gromos
forcefield to include the lipid parameters. Out of interest, Do you know
any gromacs tools or other programs that calculatg the area per lipid and
bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM but
it only works with bilyer lipids. thanks.

Merril.

On 10 Mar 2017 00:19, "Thomas Piggot"  wrote:

> Sort of. The saturated carbons after the double bond will be correct too,
> just not C9 and C10 in the double bond (as you need different assumptions
> for calculating these in united-atom system which the -unsat option is
> meant to do correctly but doesn't). Additionally, there are tools out there
> that will work for calculating the order parameters of the unsaturated bond
> if you need it.
>
> GROMOS 53A6 is not really a lipid force field per say but there are PG
> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
> lipid parameters are you using? Lots of them don't work well at all.
>
> Cheers
>
> Tom
>
> On 10/03/17 00:10, Merril Mathew wrote:
>
>> Hi,
>>
>> I am using a united atom forcefield. gromos53a6. So does that mean as long
>> as I avoid the double bond and the subsequent carbons after the double
>> bond, then the calculation is correct?  I understand it does not describe
>> the full lipid length but can be used to assess the monolayer behaviour
>> roughly.
>>
>> Merril.
>>
>> On 10 Mar 2017 12:04 a.m., "Thomas Piggot"  wrote:
>>
>> The order parameters calculated for all the saturated carbons will be
>>> correct but the gmx order program doesn't calculate the order parameters
>>> for the unsaturated carbons correctly (even when using the -unsat
>>> option).
>>>
>>> Out of interest, is this a united-atom or all-atom force field you are
>>> using?
>>>
>>> Cheers
>>>
>>> Tom
>>>
>>> On 09/03/17 23:51, Merril Mathew wrote:
>>>
>>> Hi,

 I followed turorials found on Bevanlab by Justin. I successfully
 calculated
 order parameter for DPPC molecules in my system following the tutorial.
 My
 question is whether the same calculation can be applied for a POPG
 molecule
 with a double bond in the acyl chain.? can I group all the carbon upto
 the
 double bond, therefore ignoring the double bond and the rest of the
 carbons
 in the chain to calculate order parameter? Is that a reasonable analysis
 to
 measure the order of POPG molecules.? Thanks.

 --
>>> Dr Thomas Piggot
>>> Visiting Fellow
>>> University of Southampton, UK.
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Order parameter for double bonded lipids

[Thomas Piggot]

Sort of. The saturated carbons after the double bond will be correct 
too, just not C9 and C10 in the double bond (as you need different 
assumptions for calculating these in united-atom system which the -unsat 
option is meant to do correctly but doesn't). Additionally, there are 
tools out there that will work for calculating the order parameters of 
the unsaturated bond if you need it.


GROMOS 53A6 is not really a lipid force field per say but there are PG 
compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which 
lipid parameters are you using? Lots of them don't work well at all.


Cheers

Tom

On 10/03/17 00:10, Merril Mathew wrote:

Hi,

I am using a united atom forcefield. gromos53a6. So does that mean as long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct?  I understand it does not describe
the full lipid length but can be used to assess the monolayer behaviour
roughly.

Merril.

On 10 Mar 2017 12:04 a.m., "Thomas Piggot"  wrote:


The order parameters calculated for all the saturated carbons will be
correct but the gmx order program doesn't calculate the order parameters
for the unsaturated carbons correctly (even when using the -unsat option).

Out of interest, is this a united-atom or all-atom force field you are
using?

Cheers

Tom

On 09/03/17 23:51, Merril Mathew wrote:


Hi,

I followed turorials found on Bevanlab by Justin. I successfully
calculated
order parameter for DPPC molecules in my system following the tutorial. My
question is whether the same calculation can be applied for a POPG
molecule
with a double bond in the acyl chain.? can I group all the carbon upto the
double bond, therefore ignoring the double bond and the rest of the
carbons
in the chain to calculate order parameter? Is that a reasonable analysis
to
measure the order of POPG molecules.? Thanks.


--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
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--
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Visiting Fellow
University of Southampton, UK.

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Re: [gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

Hi,

I am using a united atom forcefield. gromos53a6. So does that mean as long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct?  I understand it does not describe
the full lipid length but can be used to assess the monolayer behaviour
roughly.

Merril.

On 10 Mar 2017 12:04 a.m., "Thomas Piggot"  wrote:

> The order parameters calculated for all the saturated carbons will be
> correct but the gmx order program doesn't calculate the order parameters
> for the unsaturated carbons correctly (even when using the -unsat option).
>
> Out of interest, is this a united-atom or all-atom force field you are
> using?
>
> Cheers
>
> Tom
>
> On 09/03/17 23:51, Merril Mathew wrote:
>
>> Hi,
>>
>> I followed turorials found on Bevanlab by Justin. I successfully
>> calculated
>> order parameter for DPPC molecules in my system following the tutorial. My
>> question is whether the same calculation can be applied for a POPG
>> molecule
>> with a double bond in the acyl chain.? can I group all the carbon upto the
>> double bond, therefore ignoring the double bond and the rest of the
>> carbons
>> in the chain to calculate order parameter? Is that a reasonable analysis
>> to
>> measure the order of POPG molecules.? Thanks.
>>
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Order parameter for double bonded lipids

[Thomas Piggot]

The order parameters calculated for all the saturated carbons will be 
correct but the gmx order program doesn't calculate the order parameters 
for the unsaturated carbons correctly (even when using the -unsat option).


Out of interest, is this a united-atom or all-atom force field you are 
using?


Cheers

Tom

On 09/03/17 23:51, Merril Mathew wrote:

Hi,

I followed turorials found on Bevanlab by Justin. I successfully calculated
order parameter for DPPC molecules in my system following the tutorial. My
question is whether the same calculation can be applied for a POPG molecule
with a double bond in the acyl chain.? can I group all the carbon upto the
double bond, therefore ignoring the double bond and the rest of the carbons
in the chain to calculate order parameter? Is that a reasonable analysis to
measure the order of POPG molecules.? Thanks.


--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

--
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[gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

Hi,

I followed turorials found on Bevanlab by Justin. I successfully calculated
order parameter for DPPC molecules in my system following the tutorial. My
question is whether the same calculation can be applied for a POPG molecule
with a double bond in the acyl chain.? can I group all the carbon upto the
double bond, therefore ignoring the double bond and the rest of the carbons
in the chain to calculate order parameter? Is that a reasonable analysis to
measure the order of POPG molecules.? Thanks.
-- 
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Re: [gmx-users] Use of -nr for order parameters

[Wally Davis]

My input line is:
gmx order -s test.tpr -f fullTraj.trr -n orderParam.ndx 
The index file is formated with 3 groups, one per carbon along the chain of 
interest.
The error I get is: "In option nr  Required option was not provided, and the 
default file 'index' does not exist or is not accessible.   The following 
extensions were tried to complete the file name:  .ndx"
Every example I have seen online does not include an nr option. Any ideas on 
what this is or how to get rid of the error? 

On Wednesday, March 8, 2017 5:31 PM, Justin Lemkul  wrote:
 

 

On 3/8/17 4:46 PM, Wally Davis wrote:
> Hi,
> I'm trying to use the g_order function. I have formated my .ndx file with one 
> group per carbon and provide this file under the -n input option. However, I 
> alway get the error that the -nr file is not found. What is the extra .ndx 
> file I need to provide?
>

Please provide your full command and all relevant screen output, including the 
error.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] need help !

[Mark Abraham]

Hi,

See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

On Thu, Mar 9, 2017 at 5:04 PM  wrote:

> Thank you for yours answers .
>
> I'm a felling more comfortable.So to sum up my index file is filled with
> the coordonate that i care.
> So in my case if i want only the RNA i just have to delete all the others
> data.And when i run my .xtc for make it shorter il 'll have only water
> Or i have just to choose the RNA in the menu after using trjconv
>
>
>
> - Mail original -
> De: "Mark Abraham" 
> À: gmx-us...@gromacs.org, "gromacs org gmx-users" <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Envoyé: Jeudi 9 Mars 2017 16:30:36
> Objet: Re: [gmx-users] need help !
>
> Hi,
>
> On Thu, Mar 9, 2017 at 3:11 PM  wrote:
>
> > Hello.
> >
> > I am new on using gromacs and i have problems with my files .I need to
> > remove water and ions from an .xtc in order to keep my RNA.Then i have to
> > center the system in the box and remove some frame to be able to
> visualize
> > it.
> >
> > Here are the commands lines that i use:
> >
> > trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
> >
> > i chose only RNA
> >
> > trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> > index.ndx
> >
> > then i convert it into pdb and i remove some frame
> >
> > trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
> >
> >
> > I have a few question :
> >
> > is my code right ?
> >
>
> Seems plausible.
>
> what do we use index files ?
> >
>
> To specify the indices of subsets of atoms that are of interest.
>
>
> > How can i be sure that i have a good .tpr file because sometimes i have
> > errors.
> >
>
> If it ran your simulation, it's good.
>
> Mark
>
>
> > Tahnks you !!
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> >
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Re: [gmx-users] need help !

[electronsource]

Thank you for yours answers .

I'm a felling more comfortable.So to sum up my index file is filled with the 
coordonate that i care.
So in my case if i want only the RNA i just have to delete all the others 
data.And when i run my .xtc for make it shorter il 'll have only water 
Or i have just to choose the RNA in the menu after using trjconv 

  

- Mail original -
De: "Mark Abraham" 
À: gmx-us...@gromacs.org, "gromacs org gmx-users" 

Envoyé: Jeudi 9 Mars 2017 16:30:36
Objet: Re: [gmx-users] need help !

Hi,

On Thu, Mar 9, 2017 at 3:11 PM  wrote:

> Hello.
>
> I am new on using gromacs and i have problems with my files .I need to
> remove water and ions from an .xtc in order to keep my RNA.Then i have to
> center the system in the box and remove some frame to be able to visualize
> it.
>
> Here are the commands lines that i use:
>
> trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
>
> i chose only RNA
>
> trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> index.ndx
>
> then i convert it into pdb and i remove some frame
>
> trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
>
>
> I have a few question :
>
> is my code right ?
>

Seems plausible.

what do we use index files ?
>

To specify the indices of subsets of atoms that are of interest.


> How can i be sure that i have a good .tpr file because sometimes i have
> errors.
>

If it ran your simulation, it's good.

Mark


> Tahnks you !!
>
>
>
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Re: [gmx-users] need help !

[Mark Abraham]

Hi,

On Thu, Mar 9, 2017 at 3:11 PM  wrote:

> Hello.
>
> I am new on using gromacs and i have problems with my files .I need to
> remove water and ions from an .xtc in order to keep my RNA.Then i have to
> center the system in the box and remove some frame to be able to visualize
> it.
>
> Here are the commands lines that i use:
>
> trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
>
> i chose only RNA
>
> trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> index.ndx
>
> then i convert it into pdb and i remove some frame
>
> trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
>
>
> I have a few question :
>
> is my code right ?
>

Seems plausible.

what do we use index files ?
>

To specify the indices of subsets of atoms that are of interest.


> How can i be sure that i have a good .tpr file because sometimes i have
> errors.
>

If it ran your simulation, it's good.

Mark


> Tahnks you !!
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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[gmx-users] need help !

[electronsource]

Hello.

I am new on using gromacs and i have problems with my files .I need to remove 
water and ions from an .xtc in order to keep my RNA.Then i have to center the 
system in the box and remove some frame to be able to visualize it.

Here are the commands lines that i use:

trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx

i chose only RNA
 
trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n index.ndx

then i convert it into pdb and i remove some frame 

trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb 


I have a few question :

is my code right ?

what do we use index files ?

How can i be sure that i have a good .tpr file because sometimes i have errors.

Tahnks you !!



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Re: [gmx-users] I want to drag two atoms together with GROMCS SMD options.

[Justin Lemkul]

On 3/9/17 3:00 AM, Vytautas Rakeviius wrote:

Hello,
I want to drag two atoms together with GROMCS SMD options.But I tried different 
options and still those groups are pushed away one from another.I would be very 
thankful if someone edits this code example (from: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp)
 in such way that Chan_A and Chain_B comes together into covalent bounding rage 
or similar:; Pull code


A negative pull rate causes the two groups to approach (e.g. distance 
decreases), in contrast to the tutorial settings quoted below in which a 
positive pull rate causes a dissociation/distance increase.


-Justin


pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Performance advice for newest Pascal architecture

[Téletchéa Stéphane]

Dear colleagues,

We are willing to invest on nodes for GROMACS-specific calculations, and 
trying to best the best for our bucks (as everyone).


For now our decisions comes close to nodes using the following 
configuration:


2 * Xeon E5-2630 v4
1 P100 or 2 * P5000 or 2 * K40
Cluster node interconnection: Intel OmniPath

Our system will will range from 50k to 200k atoms most of the time, 
using AMBER-99SB-ILDn, GROMCAS 2016.1 and above.


I am aware of various benchmark and recommandations like "Best Bang for 
your Bucks", but is there any reference (internal may be) for latest 
Pascal architecture, or any general advice against/for ?


Thanks a lot in advance for the feedback, if we are able to benchmark on 
our systems using the different setups above we'll share as possible by 
the upstream vendor the results.


Stéphane

--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 
Nantes cedex 03, France

Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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[gmx-users] I want to drag two atoms together with GROMCS SMD options.

[Vytautas Rakeviius]

Hello,
I want to drag two atoms together with GROMCS SMD options.But I tried different 
options and still those groups are pushed away one from another.I would be very 
thankful if someone edits this code example (from: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp)
 in such way that Chan_A and Chain_B comes together into covalent bounding rage 
or similar:; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0
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