date:20180605

Re: [gmx-users] Charge groups in poly methyl methacrylic acid

2018-06-05 Thread Alex

I would try to double-check with topology generators like 
http://erg.biophys.msu.ru/tpp/ on a short polymer chain (e.g. three 
links, termini passivated by H), or do a CHELPG calculation to look at 
the charge distribution within the central unit (OPLS and AMBER rely on 
CHELPG charges) to get an idea. That said, if the default linkage carbon 
(139) expects passivation, within a given unit you could simply set its 
charge to zero.


None of this sounds very robust, I know, but that's sort of the LEGO 
nature of OPLS.


Alex


On 6/5/2018 9:01 PM, Debadutta Prusty wrote:

Hi everyone,

I am new to gromacs and hence, this question might be naive. How does one
go about assigning charge groups while creating new monomer topologies in
.rtp files? What I gather from looking at similar posts is that the net
charge of a charge group should be an integer (zero for a neutral group and
positive/negative for charged groups). However, this rule does not seem to
be that straight-forward in many cases. For a polymer PMAA  (
https://en.wikipedia.org/wiki/Poly(methacrylic_acid)), the charged groups
can be CO2H, CH3,CH2. According to opls fields, these groups have a net
zero charge. However, the remaining carbon atom, which does not have a
hydrogen, has a net charge of -0.02 if I use  opls_139 (C in alkane). Is
there a way around this problem ?

Thanks,
Debadutta Prusty


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[gmx-users] Charge groups in poly methyl methacrylic acid

2018-06-05 Thread Debadutta Prusty

Hi everyone,

I am new to gromacs and hence, this question might be naive. How does one
go about assigning charge groups while creating new monomer topologies in
.rtp files? What I gather from looking at similar posts is that the net
charge of a charge group should be an integer (zero for a neutral group and
positive/negative for charged groups). However, this rule does not seem to
be that straight-forward in many cases. For a polymer PMAA  (
https://en.wikipedia.org/wiki/Poly(methacrylic_acid)), the charged groups
can be CO2H, CH3,CH2. According to opls fields, these groups have a net
zero charge. However, the remaining carbon atom, which does not have a
hydrogen, has a net charge of -0.02 if I use  opls_139 (C in alkane). Is
there a way around this problem ?

Thanks,
Debadutta Prusty
-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Virtual sites causing npt simulation instabilities

2018-06-05 Thread Justin Lemkul





On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote:

Sorry about that, he’s a another link to the same files with the fixed em.mdp. 
I hope the 7zip format is ok.


Please use tgz or just upload a plain-text em.mdp.

-Justin


https://files.fm/u/r65e3kzq

Andrew E. Eisenhart
Graduate Research Assistant | University of Cincinnati
330.383.5061

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 7:05:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.


em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin




https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
 qm1   qm1 0.000   -2.516V  0.000  0.000
 qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1

Re: [gmx-users] Virtual sites causing npt simulation instabilities

2018-06-05 Thread Eisenhart, Andrew (eisenhaw)

Sorry about that, he’s a another link to the same files with the fixed em.mdp. 
I hope the 7zip format is ok.

https://files.fm/u/r65e3kzq

Andrew E. Eisenhart
Graduate Research Assistant | University of Cincinnati
330.383.5061

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 7:05:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:
> Here's the link to the files, if there's anything else I can send let me 
> know. I've been using 5.1.1 for the initial set up and energy minimization, 
> and 5.1.2 for the nvt and npt simulations.
>

em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin

> 
>
> https://files.fm/u/c9uef9qh
>
>
>
> Thanks
>
> Andrew
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: Tuesday, June 5, 2018 12:54:50 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
>
>
> On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
>> Hello again,
>>
>> I have done a few things since I last updated this list.
>>
>>
>> I generated a new system of only 1000 water instead of the original 2000, I 
>> used a more careful approach in my energy minimization, minimizing first 
>> with all bonds and angles constrained then again without those hash 
>> constraints. This succeeded in getting the maximum force in my system to 
>> below 100kcal without lincs warnings.
>>
>>
>> Then I proceeded to equilibrate the temperature as before with no issues, 
>> and finally I attempted to equilibrate the box size  using the Berendsen 
>> barostat running for 2ns. The box size increases as before and still does 
>> not converge. The system stays at around 300K, but after a while (~1ns) it 
>> seems to fill the box like its a gas visually at least.
>>
>> So any ideas that I could try would be appreciated.
> If you can assemble a tarball that contains starting coordinates (not
> minimized), topology, all .mdp files, and a run script that gives the
> exact sequence of what you're doing, and post it somewhere to share, I
> will try to take a look at it and see if I can reproduce the behavior.
>
> What version of GROMACS are you using?
>
> -Justin
>
>> Thanks,
>>
>> Andrew
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of Eisenhart, 
>> Andrew (eisenhaw) 
>> Sent: Thursday, May 31, 2018 1:51:51 PM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>>
>> Hey,
>>
>> Thanks for everyone's response.
>>
>>
>> I have tried using the berendsen barostat, with it I see similar behavior 
>> with the unit cell jumping up in size and then steadily increasing in size. 
>> I have some longer runs using it running now (2-3ns), so I'll be able to see 
>> it it eventually converges.
>>
>>
>> Nice catch with the particle type being incorrect, but with it corrected I'm 
>> still having the same problems (ie the oscillation of the box size) it has 
>> yet to throw lincs warnings though (even at ts = 2fs) so I'm going to 
>> simulate for a longer amount of time to see if it will converge.
>>
>>
>> Thanks again for everyone's reply, below is my .itp in its entirety maybe 
>> there is an error in the exceptions(which im still not 100% sure about) or 
>> something else that will stand out.
>>
>>
>> Andrew
>>
>>
>> ;
>>
>> [ atomtypes ]
>> ; name  bond_typemasscharge   ptype  sigma  epsilon
>> qm1   qm1 0.000   -2.516V  0.000  0.000
>> qh1   qh1 0.0001.258V  0.000  0.000
>>
>> [ moleculetype ]
>> ; molname   nrexcl
>> M3  3
>>
>> [ atoms ]
>> ; idat type res nr  residu name at name cg nr   charge
>> 1   opls_1131   M3  OW 1   0.0
>> 2   opls_1141   M3 HW1 1   0.0
>> 3   opls_1141   M3 HW2 1   0.0
>> 4   qm1 1   M3  qm 1  -2.516
>> 5   qh1 1   M3 qh1 1   1.258
>> 6   qh1 1   M3 qh2 1   1.258
>> #ifndef FLEXIBLE
>>
>> [ settles ]
>> ; OWfunct   dohdhh
>> 1   1   0.095720.15139
>> #else
>> [ bonds ]
>> ; i j   funct   length  force.c.
>> 1   2   1   0.09572 502416.0 0.09572502416.0
>> 1   3   1   0.09572 502416.0 0.09572502416.0
>>
>> [ angles ]
>> ; i j   k   funct   angle   force.c.
>> 2   1   3   1   104.52  628.02  104.52  628.02
>> #endif
>>
>> [ exclusions ]
>> 1   2   3   4   5   6
>> 2   1   3   4   5   6
>> 3   1   2   4   5   6
>> 4   1   2   3   5   6
>> 5   1   2   3   4   6
>> 6   1   2   3   4   5
>>
>> [

Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

2018-06-05 Thread Justin Lemkul




On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote:

Dear Gromacs Users,


I have recently started performing membrane simulations in gromacs 5.01 
version, I have started running simulations with pure POPE bilayer constructed 
from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each 
bilayer). The bilayer is solvated with 0.15 mol of KCL ( as Na ions have 
problem with lipid layers). The lipid layer is solvated with hydration number 
of 36 (lipid:water ratio).


I went through a series of literature and gromacs mailing list regarding 
decrease in area per lipid and tried different combinations but the area per 
lipid decreases by 3-4 angs from the experimental values (~58 for POPE).


I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888−3903


The APL value they obtained was 55.5 A^2, so your observations are 
consistent. The force field apparently underestimates APL slightly.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] total energy of a protein

2018-06-05 Thread Justin Lemkul




On 6/5/18 5:12 PM, Saumyak Mukherjee wrote:

Dear All,

Is there any way of obtaining the total energy of a protein from GROMACS
(including bond stretch, angle bend, dihedral, Coulomb,  LJ, Coulomb-14 and
LJ-14) other than using gmx mdrun rerun?
‌


No, because there's no built-in way to decompose the energy. This 
quantity is totally non-physical by itself.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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* 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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Re: [gmx-users] Virtual sites causing npt simulation instabilities

2018-06-05 Thread Justin Lemkul





On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.



em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin




https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
qm1   qm1 0.000   -2.516V  0.000  0.000
qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:


On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:

Hello all,

I am having an issue with the current systems I am

Re: [gmx-users] Virtual sites causing npt simulation instabilities

2018-06-05 Thread Eisenhart, Andrew (eisenhaw)

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.




https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
> Hello again,
>
> I have done a few things since I last updated this list.
>
>
> I generated a new system of only 1000 water instead of the original 2000, I 
> used a more careful approach in my energy minimization, minimizing first with 
> all bonds and angles constrained then again without those hash constraints. 
> This succeeded in getting the maximum force in my system to below 100kcal 
> without lincs warnings.
>
>
> Then I proceeded to equilibrate the temperature as before with no issues, and 
> finally I attempted to equilibrate the box size  using the Berendsen barostat 
> running for 2ns. The box size increases as before and still does not 
> converge. The system stays at around 300K, but after a while (~1ns) it seems 
> to fill the box like its a gas visually at least.
>
> So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin

> Thanks,
>
> Andrew
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Eisenhart, 
> Andrew (eisenhaw) 
> Sent: Thursday, May 31, 2018 1:51:51 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
> Hey,
>
> Thanks for everyone's response.
>
>
> I have tried using the berendsen barostat, with it I see similar behavior 
> with the unit cell jumping up in size and then steadily increasing in size. I 
> have some longer runs using it running now (2-3ns), so I'll be able to see it 
> it eventually converges.
>
>
> Nice catch with the particle type being incorrect, but with it corrected I'm 
> still having the same problems (ie the oscillation of the box size) it has 
> yet to throw lincs warnings though (even at ts = 2fs) so I'm going to 
> simulate for a longer amount of time to see if it will converge.
>
>
> Thanks again for everyone's reply, below is my .itp in its entirety maybe 
> there is an error in the exceptions(which im still not 100% sure about) or 
> something else that will stand out.
>
>
> Andrew
>
>
> ;
>
> [ atomtypes ]
> ; name  bond_typemasscharge   ptype  sigma  epsilon
>qm1   qm1 0.000   -2.516V  0.000  0.000
>qh1   qh1 0.0001.258V  0.000  0.000
>
> [ moleculetype ]
> ; molname   nrexcl
> M3  3
>
> [ atoms ]
> ; idat type res nr  residu name at name cg nr   charge
> 1   opls_1131   M3  OW 1   0.0
> 2   opls_1141   M3 HW1 1   0.0
> 3   opls_1141   M3 HW2 1   0.0
> 4   qm1 1   M3  qm 1  -2.516
> 5   qh1 1   M3 qh1 1   1.258
> 6   qh1 1   M3 qh2 1   1.258
> #ifndef FLEXIBLE
>
> [ settles ]
> ; OWfunct   dohdhh
> 1   1   0.095720.15139
> #else
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572 502416.0 0.09572502416.0
> 1   3   1   0.09572 502416.0 0.09572502416.0
>
> [ angles ]
> ; i j   k   funct   angle   force.c.
> 2   1   3   1   104.52  628.02  104.52  628.02
> #endif
>
> [ exclusions ]
> 1   2   3   4   5   6
> 2   1   3   4   5   6
> 3   1   2   4   5   6
> 4   1   2   3   5   6
> 5   1   2   3   4   6
> 6   1   2   3   4   5
>
> [ virtual_sites3 ]
> ; Vsite fromfunct   a   b
> 4   1   2   3   1   0.29869481802   0.29869481802
> ; Vsite (3fad) functtheta   d
> 5   3   2   1   3 18.060.025
> 6   2   3   1   3 18.060.025
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Mark Abraham 
> 
> Sent: Thursday, May 31, 2018 7:54:09 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
> Hi,
>
> If that fixes the issue, then please let us know - we should consider
> fixing grompp to check that the inputs have appropriate consistency.
>
> Mark
>
> On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:
>
>>
>> On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw)

[gmx-users] total energy of a protein

2018-06-05 Thread Saumyak Mukherjee

Dear All,

Is there any way of obtaining the total energy of a protein from GROMACS
(including bond stretch, angle bend, dihedral, Coulomb,  LJ, Coulomb-14 and
LJ-14) other than using gmx mdrun rerun?
‌
Regards,
Saumyak
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[gmx-users] bundling four water molecules

2018-06-05 Thread Alex

Dear all,
I wonder how I can bundle 4 water molecules together as a single object? I
heard some thing called *virtual bond* can do it in gromacs, but I could
not find any documentation about it in the manual.
I guess the virtual bond is not the virtual site in the manual.

Thank you.
Alex
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[gmx-users] Calculations of preferential interaction coefficient

2018-06-05 Thread Apramita Chand

Dear All,
I want to calculate the preferential interaction coefficient and
subsequently the Gibbs free energy of solvation for protein in water and in
water-co-solvent mixture.
1. According to the equation specified in the literature, if I can generate
a list of no. of solvent molecules (for each local/bulk region) for each
frame using g_select or g_trjconv tool in GROMACS, it will give me nw, nx
for local and bulk regions per frame.For the entire average of the equation
given, can I take these list of values and for each frame, compute the
value of interaction coefficient. Thereby, if I get a list of all such
values for every frame, I can average it to get to the value of
preferential interaction coefficient over all frames.

Is this method correct?

2. In most of the literature, the protein backbone has been considered as
reference group. Is it necessary to take COM of the backbone while giving
g_select/g_trjconv??


Please suggest


Yours sincerely,
Apramita
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[gmx-users] Doubts in g_select and g_trjconv

2018-06-05 Thread Apramita Chand

With reference to my earlier message, I have also tried the g_trjorder
command giving reference group as Backbone.

When I give the command,
g_trjorder -f 100ns_nc_72um2.xtc -s md.tpr -nshell nshell_urea.xvg -r 0.45
-da 0

I am getting reasonable no.of urea molecules like 6,8,9,etc.  Same goes for
water moelcules.

But when I add -com option, all of the numebrs decrease to 0 or 1.

So is it wrong to add -com option? Considering we're already specifying -da
as 0?

Yours sincerely,
Apramita Chand




From: Apramita Chand 
To: gmx-us...@gromacs.org
Subject: [gmx-users] Doubts regarding g_select
Message-ID:

Content-Type: text/plain; charset="UTF-8"

 Dear All,
I am confused between different commands and their outputs for g_select. I
want to choose a cutoff of 0.45nm and want to calculate the no. of urea
molecules within 0.45 as well as beyond 0.45nm of the peptide backbone.
I have a total of 18 urea molecules in my system

One of the commands:
g_select -select ' resname UREA and within 0.45 of group Backbone' -f
100nc_entire.xtc -s md.tpr -os size_within0.45_urea_backbone.xvg -oi
index_within0.45_urea_backbone.dat -oc cfrac_urea_within0.45_backbone.xvg
-seltype mol_com

gives 6,5,4,3...etc urea molecules in the size.xvg file which seems to be
correct

But if I give the same command by changing it to
g_select -select 'rdist=res_com distance from com of group Backbone;
resname UREA and rdist<=0.45'

I get 0 or 1 urea molecule for every time frame.


Again, I want to generate no.of urea molecules beyond 0.45,

Giving,
g_select -select 'rdist=res_com distance from com of group Backbone;
resname UREA and rdist<=0.45'
I get all 18 urea molecules in the above 0.45 regime


That is confusing!

I think the first command that specified within 0.45 nm is correct for my
system and I would like a similar command that can specify beyond 0.45nm.

This problem persists even when I increase urea molecules to 40 or 80.
THere's just 1 molecule below 0.45nm and all of the others above 0.45nm.
But the hydrogen bond numbers show increasing no. of hydrogen bonds between
peptide-urea (increases upto 6-9) . What could be going wrong?

Any suggestions regarding this problem?


Yours sincerely,
Apramita
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[gmx-users] Doubts regarding g_select

2018-06-05 Thread Apramita Chand

 Dear All,
I am confused between different commands and their outputs for g_select. I
want to choose a cutoff of 0.45nm and want to calculate the no. of urea
molecules within 0.45 as well as beyond 0.45nm of the peptide backbone.
I have a total of 18 urea molecules in my system

One of the commands:
g_select -select ' resname UREA and within 0.45 of group Backbone' -f
100nc_entire.xtc -s md.tpr -os size_within0.45_urea_backbone.xvg -oi
index_within0.45_urea_backbone.dat -oc cfrac_urea_within0.45_backbone.xvg
-seltype mol_com

gives 6,5,4,3...etc urea molecules in the size.xvg file which seems to be
correct

But if I give the same command by changing it to
g_select -select 'rdist=res_com distance from com of group Backbone;
resname UREA and rdist<=0.45'

I get 0 or 1 urea molecule for every time frame.


Again, I want to generate no.of urea molecules beyond 0.45,

Giving,
g_select -select 'rdist=res_com distance from com of group Backbone;
resname UREA and rdist<=0.45'
I get all 18 urea molecules in the above 0.45 regime


That is confusing!

I think the first command that specified within 0.45 nm is correct for my
system and I would like a similar command that can specify beyond 0.45nm.

This problem persists even when I increase urea molecules to 40 or 80.
THere's just 1 molecule below 0.45nm and all of the others above 0.45nm.
But the hydrogen bond numbers show increasing no. of hydrogen bonds between
peptide-urea (increases upto 6-9) . What could be going wrong?

Any suggestions regarding this problem?


Yours sincerely,
Apramita
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[gmx-users] mdp-settings for charmm36 and lipid apl values

2018-06-05 Thread Muthukumaran Rajagopalan

Dear Gromacs Users, 


I have recently started performing membrane simulations in gromacs 5.01 
version, I have started running simulations with pure POPE bilayer constructed 
from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each 
bilayer). The bilayer is solvated with 0.15 mol of KCL ( as Na ions have 
problem with lipid layers). The lipid layer is solvated with hydration number 
of 36 (lipid:water ratio).


I went through a series of literature and gromacs mailing list regarding 
decrease in area per lipid and tried different combinations but the area per 
lipid decreases by 3-4 angs from the experimental values (~58 for POPE). 


I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888−3903
Lee et al J. Chem. Theory Comput. 2016, 12, 405−413 

Klauda Jeffery B et al J. Phys. Chem. B, Vol. 114, No. 23, 2010


and previous gromacs mailing list


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-July/073351.html
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106385.html



I have used charmm36 force (default given by charmm-gui). I assume charmm-gui 
provides the charmm specific TIP3P water model (TIPs3P). The simulations start 
with a minimization with steep and CG methods for (emtol = 100.0), followed by 
a NVT simulation with restraints on P atoms of lipids ( 1 KJ/mol) for 200 
ps and gradual reduction of restraints 12 steps of NPT each for 500 ps. This is 
followed by a unrestrained run for 100 ns. I have pasted the md.mdp file 
options below

integrator = md
dt = 0.002
nsteps = 250
nstlog = 5000
nstxout = 
nstvout = 
nstcalcenergy = 100
nstenergy = 5000
nstxout-compressed = 5000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 0.8 (as per Pluhackova, K et al J. Phys. Chem. B 2016, 120, 
3888−3903 )
rvdw = 1.2

; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
coulomb-modifier = Potential-shift-Verlet (as per Pluhackova, K et al J. Phys. 
Chem. B 2016, 120, 3888−3903 )
rcoulomb-switch = 0
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
;

tcoupl = V-rescale
tc_grps = POPE SOL_ION
tau_t = 1.0 1.0
ref_t = 310.00 310.00
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
; Bond parameters
continuation = yes 
constraint_algorithm = lincs 
constraints = all-bonds 
lincs_iter = 1 
lincs_order = 4 
;
;Periodic boundary conditions
pbc = xyz ; 3-D PBC

; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme

; Velocity generation
gen_vel = no ; Velocity generation is off
 
;
nstcomm = 100
comm_mode = linear
comm_grps = System
;
refcoord_scaling = no

Any suggestions regarding the protocol followed..
 


with regards

Muthukumaran Rajagopalan
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Re: [gmx-users] Virtual sites causing npt simulation instabilities

2018-06-05 Thread Justin Lemkul





On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.


If you can assemble a tarball that contains starting coordinates (not 
minimized), topology, all .mdp files, and a run script that gives the 
exact sequence of what you're doing, and post it somewhere to share, I 
will try to take a look at it and see if I can reproduce the behavior.


What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
   qm1   qm1 0.000   -2.516V  0.000  0.000
   qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:



On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:

Hello all,

I am having an issue with the current systems I am working on. The

system consists of 2000 6point water molecules (3 chargeless masses for Ow,
hw1, and hw2; and 3 massless point charges for the electrostatics). The
three point charges I have implemented as virtual interaction sites using
the section below in my topology file.


[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025


this is loosely based on the tip4p model. Since the two partial charges

off of the hydrogens differ only in location I have them defined as a
single type with sigma

Re: [gmx-users] Box dimension

2018-06-05 Thread Viveca Lindahl

Perhaps a solution for those who don't like off-GROMACS topics, is to not
get involved in such threads? ;)

--
Viveca


On Mon, Jun 4, 2018 at 9:07 AM, Alex  wrote:

> And again, your question has nothing to do with Gromacs. It has to do with
> what you want to do, common sense, and basic arithmetic.
>
> CNTs interact at pretty short range (if they are intact and without edge
> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
> give it some additional space, say, 1 nm, and finally keep the box
> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x 2 =
> 7.6 nm. You could of course place the CNT off center (in Z) to shorten the
> box.
>
> Alex
>
>
>
> On 6/4/2018 12:53 AM, rose rahmani wrote:
>
>> Hi,
>>
>> I want to do umbrella sampling for different coordination of amino acid
>> through different distances (in Z dimension) from nanotube. The nanotube
>> axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
>> curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
>> (because the nanotube radius is 0.65nm). The initial distance of amino
>> acid
>> from nanotube is 2nm. The question is how should i choose the box Z
>> dimension that some artifacts (justin explained in tutorial) doesn't
>> happen? I choose 7nm, is it ok or large?
>>
>> Would you please help me?
>>
>> Best regards
>> -Rose
>>
>
> --
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>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Virtual sites causing npt simulation instabilities

2018-06-05 Thread Eisenhart, Andrew (eisenhaw)

Hello again,

I have done a few things since I last updated this list.

I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.

Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

Thanks,

Andrew

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, 
Andrew (eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.

I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.

Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.

Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.

Andrew

;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
  qm1   qm1 0.000   -2.516V  0.000  0.000
  qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:

>
>
> On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:
> > Hello all,
> >
> > I am having an issue with the current systems I am working on. The
> system consists of 2000 6point water molecules (3 chargeless masses for Ow,
> hw1, and hw2; and 3 massless point charges for the electrostatics). The
> three point charges I have implemented as virtual interaction sites using
> the section below in my topology file.
> >
> >
> > [ virtual_sites3 ]
> > ; Vsite fromfunct   a   b
> > 4   1   2   3   1   0.29869481802   0.29869481802
> > ; Vsite (3fad) functtheta   d
> > 5   3   2   1   3 18.060.025
> > 6   2   3   1   3 18.060.025
> >
> >
> > this is loosely based on the tip4p model. Since the two partial charges
> off of the hydrogens differ only in location I have them defined as a
> single type with sigma and epsilon defined as 0. I have also done this to
> the partial charge off of the oxygen. This is all seen below in my
> atomtypes and atoms sections.
> >
> >
> > [ atomtypes ]
> > ; name  bond_typemasscharge   ptype  sigma  epsilon
> >qm1   qm1 0.000   -2.516A  0.000  0.000
> >

Re: [gmx-users] spc.itp file and flexspc.itp

2018-06-05 Thread Justin Lemkul




On 6/5/18 8:48 AM, Anjana Jayasinghe wrote:

  Dear Prof. Justin and Gromacs users,
Thank you very much for the reply. I  noticed that FLEX_SPC is defined in the 
.top file of the bilayer simulations for CiEj systems ( in 
patrickfuchs/CiEj_2016H66 ). They used a modified force field known as 2016H66 
with Gromacs 4.0.7. I am also trying to use it for my CiEj system with Gromacs 
2016 version. Since they have achieved the lamellar region by defining the 
FLEX_SPC, do I have to use the same FLEX_SPC in my .top?
Could you please comment on this.


When reproducing previous work, yes, you should do exactly as the 
authors did.


However, GROMACS 4.0.7 is wildly outdated and that's why you should note 
that "flexspc.itp" no longer exists, but you can in fact use a flexible 
SPC model by using the standard "spc.itp" with "define = -DFLEXIBLE." 
They are functionally identical.


-Justin


Thank you.

|
|
|
|  |  |

  |

  |
|
|  |
patrickfuchs/CiEj_2016H66

CiEj_2016H66 - This repositery contains files to simulate CiEj surfactants 
using the GROMOS-compatible 2016H66 f...
  |

  |

  |



 On Monday, 4 June 2018, 10:05:12 pm AEST, Justin Lemkul  
wrote:
  
  


On 6/4/18 6:13 AM, Anjana Jayasinghe wrote:

Dear Gromacs Users,
Is there any difference in the simulation, if we define the spc.itp as,

| #ifdef FLEX_SPC |
|  | #include "flexspc.itp" |
|  | #else |
|  | #include "spc.itp" |
|  | #endif |


instead of using the single line  #include "spc.itp" ?
Can anyone help me to understand the difference?

Have you looked at the contents of flexspc.itp? You'll note that it has
no functional content as this was an old way of defining flexible water.
Don't do what you have shown above. If you want flexible water, use
"define = -DFLEXIBLE" and the normal spc.itp in your topology. Again,
inspect that file's contents to understand what it is doing.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] spc.itp file and flexspc.itp

2018-06-05 Thread Anjana Jayasinghe

 Dear Prof. Justin and Gromacs users, 
Thank you very much for the reply. I  noticed that FLEX_SPC is defined in the 
.top file of the bilayer simulations for CiEj systems ( in 
patrickfuchs/CiEj_2016H66 ). They used a modified force field known as 2016H66 
with Gromacs 4.0.7. I am also trying to use it for my CiEj system with Gromacs 
2016 version. Since they have achieved the lamellar region by defining the 
FLEX_SPC, do I have to use the same FLEX_SPC in my .top?
Could you please comment on this.
Thank you. 

| 
| 
| 
|  |  |

 |

 |
| 
|  | 
patrickfuchs/CiEj_2016H66

CiEj_2016H66 - This repositery contains files to simulate CiEj surfactants 
using the GROMOS-compatible 2016H66 f...
 |

 |

 |

On Monday, 4 June 2018, 10:05:12 pm AEST, Justin Lemkul  
wrote:  

On 6/4/18 6:13 AM, Anjana Jayasinghe wrote:
> Dear Gromacs Users,
> Is there any difference in the simulation, if we define the spc.itp as,
>
> | #ifdef FLEX_SPC |
> |  | #include "flexspc.itp" |
> |  | #else |
> |  | #include "spc.itp" |
> |  | #endif |
>
>
> instead of using the single line  #include "spc.itp" ?
> Can anyone help me to understand the difference?

Have you looked at the contents of flexspc.itp? You'll note that it has 
no functional content as this was an old way of defining flexible water. 
Don't do what you have shown above. If you want flexible water, use 
"define = -DFLEXIBLE" and the normal spc.itp in your topology. Again, 
inspect that file's contents to understand what it is doing.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] regarding rmsd calculation

2018-06-05 Thread Justin Lemkul





On 6/5/18 3:05 AM, SHAHEE ISLAM wrote:

hello sir,
there are two proteins in a water box system.i am doing martini
protein cg simulation and following this tutorial
http://cgmartini.nl/index.php/tutorials-general-introduction/protein
at the 7 no step i have done
  grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr
  mdrun -deffnm dynamic -v
and run for 1 micro second.from this i have got
dynamic.xtc,dynamic.gro,dynamic.edr,dynamic.log,dynamic.cpt,dynamic_prev.cpt
and to go for continuting of the simulation from 1 to 2 microsecond i have done
  grompp -f dynamic.mdp -c dynamic.gro -p system.top -o dynamic1.tpr
  mdrun -deffnm dynamic1 -v
from the visual inspection there is not that much of difference
between the two .xtc file.
did i have done any wrong for the continuity of the simulation.


Yes, you failed to provide a checkpoint file to -t when invoking grompp 
the second time, so your system did not preserve its state. You 
shouldn't use grompp to extend a simulation unless you need to change 
something about the settings; the easiest way to extend is with 
convert-tpr (tpbconv in old versions). Instructions are on the GROMACS 
website.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] How to add distance and angle restraints in the topology file?

2018-06-05 Thread Justin Lemkul

On 6/5/18 3:50 AM, Qing Liu wrote:

Hello, everyone,
I just used Gromacs-5.1.4 to run a MD with distance and angle restraints. These restraints are
between a protein and a ligand. However, the ligand topology is included in the "ligand.itp", and
its atom numbers begin from 1. This is same as the protein atom numbers. As a result, Gromacs can not
distinguish the ligand atoms and protein atoms in the sections "distance_restraints" and
"angle_restraints". I also try to merge the topology of protein and ligand into a single file,
where the ligand atom numbers are renumbered to be consecutive from the last protein atom. But this also does
not work. Can you help me? Thank you!

Put an [intermolecular_interactions] directive at the very end of your
.top and then use [distance_restraints] and [angle_restraints]
directives under it. Use global atom numbers (from the coordinate file,
not the per-moleculetype numbering) to specify the interactions.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Extension on different machines (CPU/GPU

2018-06-05 Thread Nicolas Cheron

Hi Mark,

Thank you for the quick answer. However, the problem is not only a problem
of reproducibility of a single simulation. To make sure that I have
converged results with proper sampling, I am performing each time 10
simulations of the same system with different positions of the solvent
molecules and different initial velocities. For the 10 simulations, I had
reached a plateau at 250ns for the parameters I am looking at. When
extending to the GPU machine, for the 10 simulations I see these parameters
increasing. For other sets of simulations with the same solute but
different water:glycerol molar fractions, the plateau stays stable until
300ns and I never saw this kind of increase. That's why I was wondering if
there is a big red flag when extending simulations on another machine or
switching from CPU to GPU.

Thank you.

Nicolas

Le mar. 5 juin 2018 à 10:43, Mark Abraham  a
écrit :

> Hi,
>
> You'll basically never get a reproducible trajectory
> http://www.gromacs.org/Documentation/Terminology/Reproducibility. If your
> conclusions would depend on the configurations in any single trajectory,
> you'll have a hard time demonstrating that those conclusions are valid
> reflection of reality.
>
> Mark
>
> On Tue, Jun 5, 2018 at 10:37 AM Nicolas Cheron <
> nicolas.cheron.bou...@gmail.com> wrote:
>
> > Dear all,
> >
> > I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs.
> I
> > then wanted to extend the simulation to 300ns, and copied the .tpr and
> the
> > .cpt to another machine with GPUs (also running Gromacs 5.1.2). I
> observed
> > strange results, so I decided to also extend the simulation (from 250ns)
> on
> > the first machine to compare.
> >
> > Different results are obtained for the 2 extensions (that were started
> from
> > the same .tpr and .cpt) on the 2 different machines/architectures. Is it
> a
> > known behaviour, and one should never proceed like this? Is it due to
> > CPU/GPU, or only the fact that machines are different and the same would
> > have happened on another CPU machine?
> >
> > Thank you
> >
> > Nicolas
> >
> > PS: I am looking at a solute in a water:glycerol mixture. By "different
> > results" I mean that the number of water (or glycerol) around the solute
> > are different at all time steps
> > --
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Re: [gmx-users] mdrun -rerun

2018-06-05 Thread Mark Abraham

Hi,

Rerun post-processes the trajectory. If it could guess about frames that
aren't there, then you wouldn't need to have run the simulation. ;-)

Mark

On Tue, Jun 5, 2018 at 10:43 AM venkat  wrote:

> Hi,
> For my work, I did  md simulations (200ns)  by setting with
> 0.5 ns xtc and 0.5  ns trr files (interval used to save the coordinates).
> But now  I require 4000 frame for 200 ns MD simulations trajectory  (25000
> steps, 500 ps)  is that possible to get from using "*-rerun*"  option or
> need to run freshly ?.
>
> Thanks in Advance
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[gmx-users] mdrun -rerun

2018-06-05 Thread venkat

Hi,
For my work, I did  md simulations (200ns)  by setting with
0.5 ns xtc and 0.5  ns trr files (interval used to save the coordinates).
But now  I require 4000 frame for 200 ns MD simulations trajectory  (25000
steps, 500 ps)  is that possible to get from using "*-rerun*"  option or
need to run freshly ?.

Thanks in Advance
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Re: [gmx-users] Extension on different machines (CPU/GPU

2018-06-05 Thread Mark Abraham

Hi,

You'll basically never get a reproducible trajectory
http://www.gromacs.org/Documentation/Terminology/Reproducibility. If your
conclusions would depend on the configurations in any single trajectory,
you'll have a hard time demonstrating that those conclusions are valid
reflection of reality.

Mark

On Tue, Jun 5, 2018 at 10:37 AM Nicolas Cheron <
nicolas.cheron.bou...@gmail.com> wrote:

> Dear all,
>
> I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. I
> then wanted to extend the simulation to 300ns, and copied the .tpr and the
> .cpt to another machine with GPUs (also running Gromacs 5.1.2). I observed
> strange results, so I decided to also extend the simulation (from 250ns) on
> the first machine to compare.
>
> Different results are obtained for the 2 extensions (that were started from
> the same .tpr and .cpt) on the 2 different machines/architectures. Is it a
> known behaviour, and one should never proceed like this? Is it due to
> CPU/GPU, or only the fact that machines are different and the same would
> have happened on another CPU machine?
>
> Thank you
>
> Nicolas
>
> PS: I am looking at a solute in a water:glycerol mixture. By "different
> results" I mean that the number of water (or glycerol) around the solute
> are different at all time steps
> --
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[gmx-users] Extension on different machines (CPU/GPU

2018-06-05 Thread Nicolas Cheron

Dear all,

I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. I
then wanted to extend the simulation to 300ns, and copied the .tpr and the
.cpt to another machine with GPUs (also running Gromacs 5.1.2). I observed
strange results, so I decided to also extend the simulation (from 250ns) on
the first machine to compare.

Different results are obtained for the 2 extensions (that were started from
the same .tpr and .cpt) on the 2 different machines/architectures. Is it a
known behaviour, and one should never proceed like this? Is it due to
CPU/GPU, or only the fact that machines are different and the same would
have happened on another CPU machine?

Thank you

Nicolas

PS: I am looking at a solute in a water:glycerol mixture. By "different
results" I mean that the number of water (or glycerol) around the solute
are different at all time steps
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Re: [gmx-users] keep the size of simulation box constant in one direction

2018-06-05 Thread Alex


http://manual.gromacs.org/online/mdp_opt.html#pc

pcoupltype = semiisotropic

and set zero compressibility in the z-direction.

Alex


On 6/5/2018 2:25 AM, 凌未风 wrote:

Hi there,

I am simulating a membrane using charmm force field, unfortunately I always 
found huge fluctuation of the box size. I am wondering whether it is possible 
to fix the box size in the z direction, and allow pressure coupling in xy 
directions? How could we set up this in the mdp files?

Thanks a lot for your time and help.

Sincerely yours,
Ruoxu Gu


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[gmx-users] keep the size of simulation box constant in one direction

2018-06-05 Thread ??????

Hi there, 

I am simulating a membrane using charmm force field, unfortunately I always 
found huge fluctuation of the box size. I am wondering whether it is possible 
to fix the box size in the z direction, and allow pressure coupling in xy 
directions? How could we set up this in the mdp files?

Thanks a lot for your time and help. 

Sincerely yours, 
Ruoxu Gu
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Re: [gmx-users] How to add distance and angle restraints in the topology file?

2018-06-05 Thread Qinghua Liao

Hello,

I guess you should add your ligand.itp to aminoacids.rtp, and then use
pdb2gmx to generate a combined topology file.
After that, you can use distance or angle restraints between the protein
and the ligand.

Maybe you can try to parmed from Amber to combine your protein and
ligand topology. I never tried, but it might work.

All the best,
Qinghua

On 06/05/2018 09:50 AM, Qing Liu wrote:

Best wishes,

Qing Liu

Fudan Univ.

E-mail: 15110700...@fudan.edu.cn

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[gmx-users] How to add distance and angle restraints in the topology file?

2018-06-05 Thread Qing Liu

Hello, everyone,
I just used Gromacs-5.1.4 to run a MD with distance and angle 
restraints. These restraints are between a protein and a ligand. However, the 
ligand topology is included in the "ligand.itp", and its atom numbers begin 
from 1. This is same as the protein atom numbers. As a result, Gromacs can not 
distinguish the ligand atoms and protein atoms in the sections 
"distance_restraints" and "angle_restraints". I also try to merge the topology 
of protein and ligand into a single file, where the ligand atom numbers are 
renumbered to be consecutive from the last protein atom. But this also does not 
work.  Can you help me? Thank you!






--


Best wishes, 



Qing Liu

Fudan Univ.

E-mail: 15110700...@fudan.edu.cn
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[gmx-users] regarding free energy perturbation

2018-06-05 Thread zhangw

Hello everyone:
Is there  anyone who can perturb a portion of a molecule or protein when you do 
FEP analysis ? 
May you help me to solve the problem ?
Many Thanks!

Best regards





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Re: [gmx-users] regarding rmsd calculation

2018-06-05 Thread SHAHEE ISLAM

sorry to forget about the recentering of the .xtc file.after getting
the dynamic.xtc file i just recenter the .xtc file before doing rmsd
analysis.

On 6/5/18, SHAHEE ISLAM  wrote:
> hello sir,
> there are two proteins in a water box system.i am doing martini
> protein cg simulation and following this tutorial
> http://cgmartini.nl/index.php/tutorials-general-introduction/protein
> at the 7 no step i have done
>  grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr
>  mdrun -deffnm dynamic -v
> and run for 1 micro second.from this i have got
> dynamic.xtc,dynamic.gro,dynamic.edr,dynamic.log,dynamic.cpt,dynamic_prev.cpt
> and to go for continuting of the simulation from 1 to 2 microsecond i have
> done
>  grompp -f dynamic.mdp -c dynamic.gro -p system.top -o dynamic1.tpr
>  mdrun -deffnm dynamic1 -v
> from the visual inspection there is not that much of difference
> between the two .xtc file.
> did i have done any wrong for the continuity of the simulation.
> thanking you
> shahee
>
> On 6/4/18, Justin Lemkul  wrote:
>>
>>
>> On 6/4/18 8:57 AM, SHAHEE ISLAM wrote:
>>> hi,
>>> i am doing thr rmsd calculation of protein,by using the command
>>> gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
>>> ../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns   (this is for first 1
>>> microsecond)
>>> then again i have done for the next 1 micro second
>>> gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic1.tpr -f
>>> ../pbc.xtc/md-1-2.xtc -o rmsd-p1-1-2.xvg -tu ns (i.e from 1 to 2
>>> microsecond)
>>> but the problem is there is no continuity between the last valu of
>>> rmsd-p1-0-1.xvg and last value of rmsd-p1-1-1.xvg
>>>
>>> rmsd-p1-0-1.xvg
>>>   0.0000.0049827
>>> 0.0200.1721005
>>> 0.0400.2209484
>>> 0.0600.2384352
>>> .
>>> .
>>> .
>>>
>>> 999.94006350.8320900
>>>   999.96002200.8242129
>>>   999.98004150.8163539
>>> 1000.6100.8269945
>>>
>>> and the rmsd-p1-1-1.xvg
>>> 0.0000.0049169
>>> 0.0200.1181309
>>> 0.0400.1274706
>>> 0.0600.1289782
>>> .
>>> .
>>> .
>>> 999.94006350.5308270
>>>   999.96002200.5303858
>>>   999.98004150.5313085
>>> 1000.6100.5300161
>>
>> The fact that your time values restarted suggests that the simulation
>> did not continue from the previous time, rather it restarted from zero
>> and you have essentially two separate simulations of 1 microsecond. What
>> does visual inspection of the trajectory tell you?
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a
>> mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] regarding rmsd calculation

2018-06-05 Thread SHAHEE ISLAM

hello sir,
there are two proteins in a water box system.i am doing martini
protein cg simulation and following this tutorial
http://cgmartini.nl/index.php/tutorials-general-introduction/protein
at the 7 no step i have done
 grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr
 mdrun -deffnm dynamic -v
and run for 1 micro second.from this i have got
dynamic.xtc,dynamic.gro,dynamic.edr,dynamic.log,dynamic.cpt,dynamic_prev.cpt
and to go for continuting of the simulation from 1 to 2 microsecond i have done
 grompp -f dynamic.mdp -c dynamic.gro -p system.top -o dynamic1.tpr
 mdrun -deffnm dynamic1 -v
from the visual inspection there is not that much of difference
between the two .xtc file.
did i have done any wrong for the continuity of the simulation.
thanking you
shahee

On 6/4/18, Justin Lemkul  wrote:
>
>
> On 6/4/18 8:57 AM, SHAHEE ISLAM wrote:
>> hi,
>> i am doing thr rmsd calculation of protein,by using the command
>> gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
>> ../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns   (this is for first 1
>> microsecond)
>> then again i have done for the next 1 micro second
>> gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic1.tpr -f
>> ../pbc.xtc/md-1-2.xtc -o rmsd-p1-1-2.xvg -tu ns (i.e from 1 to 2
>> microsecond)
>> but the problem is there is no continuity between the last valu of
>> rmsd-p1-0-1.xvg and last value of rmsd-p1-1-1.xvg
>>
>> rmsd-p1-0-1.xvg
>>   0.0000.0049827
>> 0.0200.1721005
>> 0.0400.2209484
>> 0.0600.2384352
>> .
>> .
>> .
>>
>> 999.94006350.8320900
>>   999.96002200.8242129
>>   999.98004150.8163539
>> 1000.6100.8269945
>>
>> and the rmsd-p1-1-1.xvg
>> 0.0000.0049169
>> 0.0200.1181309
>> 0.0400.1274706
>> 0.0600.1289782
>> .
>> .
>> .
>> 999.94006350.5308270
>>   999.96002200.5303858
>>   999.98004150.5313085
>> 1000.6100.5300161
>
> The fact that your time values restarted suggests that the simulation
> did not continue from the previous time, rather it restarted from zero
> and you have essentially two separate simulations of 1 microsecond. What
> does visual inspection of the trajectory tell you?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] Charge groups in poly methyl methacrylic acid

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Re: [gmx-users] Virtual sites causing npt simulation instabilities

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Re: [gmx-users] Virtual sites causing npt simulation instabilities

Re: [gmx-users] Box dimension

Re: [gmx-users] Virtual sites causing npt simulation instabilities

Re: [gmx-users] spc.itp file and flexspc.itp

Re: [gmx-users] spc.itp file and flexspc.itp

Re: [gmx-users] regarding rmsd calculation

Re: [gmx-users] How to add distance and angle restraints in the topology file?

Re: [gmx-users] Extension on different machines (CPU/GPU

Re: [gmx-users] mdrun -rerun

[gmx-users] mdrun -rerun

Re: [gmx-users] Extension on different machines (CPU/GPU

[gmx-users] Extension on different machines (CPU/GPU

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[gmx-users] keep the size of simulation box constant in one direction

Re: [gmx-users] How to add distance and angle restraints in the topology file?

[gmx-users] How to add distance and angle restraints in the topology file?

[gmx-users] regarding free energy perturbation

Re: [gmx-users] regarding rmsd calculation

Re: [gmx-users] regarding rmsd calculation

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