Re: [gmx-users] Problem in protein ligand interaction

[Du, Yu]

Hi Cristina, 

Previous ultra-long conventional molecular dynamics works have shown that 
ligand can find its binding pocket and finally bind in a crystal complex pose. 
Also enhance sampling techniques, e.g. metadynamics, can speeed the binding 
process. 

So, if you want ligand to find its binding pocket, you may need long-time 
simulation or enhance sampling. 

Distance restraint on the ligand is harmonic force, it indeed can affect the 
interaction between ligand and protein.

> -原始邮件-
> 发件人: "Gonzalez Fernandez, Cristina" 
> 发送时间: 2020-03-20 17:59:05 (星期五)
> 收件人: "gmx-us...@gromacs.org" 
> 抄送: 
> 主题: [gmx-users] Problem in protein ligand interaction
> 
> Dear Gromacs users,
> 
> 
> I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, 
> it seems that the lipid does't have enough driving force to reach the binding 
> pocket, since van der Waals forces move the lipind towards the binding pocket 
> whereas electrostatics move the lipid in the opposite direction. How could I 
> achieve that the lipid reaches the protein binding site? Could I include some 
> distance restraints that help the lipid to move to the binding pocket and 
> then switch them off or this idea would lead to unreliabe results?
> 
> 
> Thank you in advance for all your help!
> 
> 
> Regards,
> 
> 
> Cristina
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] Cell Membrane Potential

[Du, Yu]

Hi Frank, 

I have never conducted any simulation on membrane potential, but you reminded 
me of the fact that many molecular dynamics simulations on membrane proteins do 
not consider the membrane potential which is ubiquitous and versatile in 
biological environment. 

If the membrane potential is a factor in your study, as it's in voltage-gated 
ion channel system, please refer to previous research papers and the following 
links:

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#electric-fields
 
http://manual.gromacs.org/documentation/current/reference-manual/special/electric-fields.html


> -原始邮件-
> 发件人: "Frank Lam" 
> 发送时间: 2020-01-30 03:55:17 (星期四)
> 收件人: gromacs.org_gmx-users@maillist.sys.kth.se
> 抄送: 
> 主题: [gmx-users] Cell Membrane Potential
> 
> Hi,
> 
> I am undergraduate student wanting to learn and use GROMACS for a project
> on membrane proteins. Is altering membrane potential in a simulation
> possible using GROMACS? I do apologize if this is trivial. I tried looking
> at the documentation, but most of the information are currently too
> challenging for me. Any guidance would be greatly appreciated.
> 
> kind regards,
> Frank
> -- 
> 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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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
Gromacs Users mailing list

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Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

[Du, Yu]

Hi Billy, 

Thanks for your remind. I indeed used the all-atom topology of melatonin from 
ATB 
(offers both all- and united- atom versions for small molecules). I will change 
to 
the united-atom version.

Sincerely,
Yu


> -Original Messages-
> From: "Billy Williams-Noonan" 
> Sent Time: 2019-10-20 11:45:40 (Sunday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under 
> all-bonds contraints?
> 
> Hi Yu,
> 
> I don't think the methyl group should have hydrogens explicitly specified
> with the Gromos force field. The methyl group should be one united atom
> 
> The methylene group is okay though.
> 
> Cheers,
> Billy
> 
> On Sat., 19 Oct. 2019, 1:06 pm Du, Yu,  wrote:
> 
> > Dear GMX-Users,
> >
> > The vibration of the hydrogens of methyl and methylene groups was the
> > result of
> > Trajectory Smoothing in VMD, not the problem of GROMACS's all-bond
> > constraints.
> >
> > Sorry for this distracting question.
> >
> > Yu
> >
> >
> > > -Original Messages-
> > > From: "Du, Yu" 
> > > Sent Time: 2019-10-18 08:20:10 (Friday)
> > > To: gmx-us...@gromacs.org
> > > Cc:
> > > Subject: Re: Re: [gmx-users] Hydrogens of ATB ligand show obvious
> > vibration under all-bonds contraints?
> > >
> > > Hi Justin,
> > >
> > > Thanks for your reply.
> > > I will use the united-atom topology of the ligand.
> > >
> > > Yu
> > >
> > >
> > > > -Original Messages-
> > > > From: "Justin Lemkul" 
> > > > Sent Time: 2019-10-17 23:17:47 (Thursday)
> > > > To: gmx-us...@gromacs.org
> > > > Cc:
> > > > Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious
> > vibration under all-bonds contraints?
> > > >
> > > >
> > > >
> > > > On 10/17/19 11:02 AM, Du, Yu wrote:
> > > > > Dear GMX-Users,
> > > > >
> > > > > I'm using GMX2018.3 simulating Melatonin (ATB Link:
> > https://atb.uq.edu.au/molecule.py?molid=355098).
> > > > >
> > > > >
> > > > > I found that the hydrogens of two methyl groups (CH3, i.e. CH11,
> > CH12, CH13, CH14, CH15 and CH16) showed
> > > > > obvious vibration under the following mdp configuration:
> > > > >
> > > > >
> > > > > integrator  = md
> > > > > dt   = 0.002
> > > > > cutoff-scheme= group
> > > > > constraints = all-bonds
> > > > > constraint_algorithm = lincs
> > > > > continuation  = yes
> > > > >
> > > > >
> > > > > I used the gromos54a7_atb.ff.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > P.S. The partial topology of Melatonin from ATB
> > > >
> > > > You're using the wrong topology. GROMOS parameter sets are
> > united-atom,
> > > > but you've chosen the all-atom topology (no idea why this exists,
> > > > honestly). Your CH3 and CH2 groups should have no explicit H atoms.
> > > >
> > > > -Justin
> > > >
> > > > > [ moleculetype ]
> > > > > ; Name   nrexcl
> > > > > ESV6 3
> > > > > [ atoms ]
> > > > > ;  nr  type  resnr  resid  atom  cgnr  chargemass
> > > > >  1HC1ESV6H1610.067   1.0080
> > > > >  2  CPos1ESV6C1320.010  12.0110
> > > > >  3HC1ESV6H1430.067   1.0080
> > > > >  4HC1ESV6H1540.067   1.0080
> > > > >  5OE1ESV6 O15   -0.368  15.9994
> > > > >  6  CAro1ESV6 C960.398  12.0110
> > > > >  7  CAro1ESV6 C77   -0.385  12.0110
> > > > >  8HC1ESV6 H780.163   1.0080
> > > > >  9  CAro1ESV6 C290.085  12.0110
> > > > > 10  CAro1ESV6 C1   10   -0.057  12.0110
> > > > > 11  CAro1ESV6 C5   11   -0.144  12.0110
> > > > > 12HC1ESV6 H3   120.186   1.0080
> > > > > 13  NOpt1ESV6 N1   13   -0.354  14.0067
> > > > > 14  

Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

[Du, Yu]

Dear GMX-Users,

The vibration of the hydrogens of methyl and methylene groups was the result of 
Trajectory Smoothing in VMD, not the problem of GROMACS's all-bond constraints.

Sorry for this distracting question.

Yu


> -Original Messages-
> From: "Du, Yu" 
> Sent Time: 2019-10-18 08:20:10 (Friday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration 
> under all-bonds contraints?
> 
> Hi Justin, 
> 
> Thanks for your reply.
> I will use the united-atom topology of the ligand.
> 
> Yu
> 
> 
> > -Original Messages-
> > From: "Justin Lemkul" 
> > Sent Time: 2019-10-17 23:17:47 (Thursday)
> > To: gmx-us...@gromacs.org
> > Cc: 
> > Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration 
> > under all-bonds contraints?
> > 
> > 
> > 
> > On 10/17/19 11:02 AM, Du, Yu wrote:
> > > Dear GMX-Users,
> > >
> > > I'm using GMX2018.3 simulating Melatonin (ATB Link: 
> > > https://atb.uq.edu.au/molecule.py?molid=355098).
> > >
> > >
> > > I found that the hydrogens of two methyl groups (CH3, i.e. CH11, CH12, 
> > > CH13, CH14, CH15 and CH16) showed
> > > obvious vibration under the following mdp configuration:
> > >
> > >
> > > integrator  = md
> > > dt   = 0.002
> > > cutoff-scheme= group
> > > constraints = all-bonds
> > > constraint_algorithm = lincs
> > > continuation  = yes
> > >
> > >
> > > I used the gromos54a7_atb.ff.
> > >
> > >
> > >
> > >
> > > P.S. The partial topology of Melatonin from ATB
> > 
> > You're using the wrong topology. GROMOS parameter sets are united-atom, 
> > but you've chosen the all-atom topology (no idea why this exists, 
> > honestly). Your CH3 and CH2 groups should have no explicit H atoms.
> > 
> > -Justin
> > 
> > > [ moleculetype ]
> > > ; Name   nrexcl
> > > ESV6 3
> > > [ atoms ]
> > > ;  nr  type  resnr  resid  atom  cgnr  chargemass
> > >  1HC1ESV6H1610.067   1.0080
> > >  2  CPos1ESV6C1320.010  12.0110
> > >  3HC1ESV6H1430.067   1.0080
> > >  4HC1ESV6H1540.067   1.0080
> > >  5OE1ESV6 O15   -0.368  15.9994
> > >  6  CAro1ESV6 C960.398  12.0110
> > >  7  CAro1ESV6 C77   -0.385  12.0110
> > >  8HC1ESV6 H780.163   1.0080
> > >  9  CAro1ESV6 C290.085  12.0110
> > > 10  CAro1ESV6 C1   10   -0.057  12.0110
> > > 11  CAro1ESV6 C5   11   -0.144  12.0110
> > > 12HC1ESV6 H3   120.186   1.0080
> > > 13  NOpt1ESV6 N1   13   -0.354  14.0067
> > > 14  HS141ESV6 H6   140.373   1.0080
> > > 15  CAro1ESV6 C4   150.070  12.0110
> > > 16  CAro1ESV6 C8   16   -0.145  12.0110
> > > 17HC1ESV6 H8   170.156   1.0080
> > > 18  CAro1ESV6C10   18   -0.360  12.0110
> > > 19HC1ESV6 H9   190.169   1.0080
> > > 20 C1ESV6 C3   20   -0.159  12.0110
> > > 21HC1ESV6 H1   210.070   1.0080
> > > 22HC1ESV6 H2   220.070   1.0080
> > > 23  CPos1ESV6 C6   230.231  12.0110
> > > 24HC1ESV6 H4   240.014   1.0080
> > > 25HC1ESV6 H5   250.014   1.0080
> > > 26 N1ESV6 N2   26   -0.525  14.0067
> > > 27  HS141ESV6H10   270.307   1.0080
> > > 28  CPos1ESV6C11   280.684  12.0110
> > > 29 OEOpt1ESV6 O2   29   -0.616  15.9994
> > > 30 C1ESV6C12   30   -0.586  12.0110
> > > 31HC1ESV6H11   310.166   1.0080
> > > 32HC1ESV6H12   320.166   1.0080
> > > 33HC1ESV6H13   330.166   1.0080
> > > ; total charge of the molecule:   0.000
> > > [ bonds ]
> > > ;  ai   aj  funct   c0 c1
> > >  122   0.1090   1.2300e+07
> > >  232   0.1090   1.2300e+07
> > >  242  

Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

[Du, Yu]

Hi Justin, 

Thanks for your reply.
I will use the united-atom topology of the ligand.

Yu


> -Original Messages-
> From: "Justin Lemkul" 
> Sent Time: 2019-10-17 23:17:47 (Thursday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under 
> all-bonds contraints?
> 
> 
> 
> On 10/17/19 11:02 AM, Du, Yu wrote:
> > Dear GMX-Users,
> >
> > I'm using GMX2018.3 simulating Melatonin (ATB Link: 
> > https://atb.uq.edu.au/molecule.py?molid=355098).
> >
> >
> > I found that the hydrogens of two methyl groups (CH3, i.e. CH11, CH12, 
> > CH13, CH14, CH15 and CH16) showed
> > obvious vibration under the following mdp configuration:
> >
> >
> > integrator  = md
> > dt   = 0.002
> > cutoff-scheme= group
> > constraints = all-bonds
> > constraint_algorithm = lincs
> > continuation  = yes
> >
> >
> > I used the gromos54a7_atb.ff.
> >
> >
> >
> >
> > P.S. The partial topology of Melatonin from ATB
> 
> You're using the wrong topology. GROMOS parameter sets are united-atom, 
> but you've chosen the all-atom topology (no idea why this exists, 
> honestly). Your CH3 and CH2 groups should have no explicit H atoms.
> 
> -Justin
> 
> > [ moleculetype ]
> > ; Name   nrexcl
> > ESV6 3
> > [ atoms ]
> > ;  nr  type  resnr  resid  atom  cgnr  chargemass
> >  1HC1ESV6H1610.067   1.0080
> >  2  CPos1ESV6C1320.010  12.0110
> >  3HC1ESV6H1430.067   1.0080
> >  4HC1ESV6H1540.067   1.0080
> >  5OE1ESV6 O15   -0.368  15.9994
> >  6  CAro1ESV6 C960.398  12.0110
> >  7  CAro1ESV6 C77   -0.385  12.0110
> >  8HC1ESV6 H780.163   1.0080
> >  9  CAro1ESV6 C290.085  12.0110
> > 10  CAro1ESV6 C1   10   -0.057  12.0110
> > 11  CAro1ESV6 C5   11   -0.144  12.0110
> > 12HC1ESV6 H3   120.186   1.0080
> > 13  NOpt1ESV6 N1   13   -0.354  14.0067
> > 14  HS141ESV6 H6   140.373   1.0080
> > 15  CAro1ESV6 C4   150.070  12.0110
> > 16  CAro1ESV6 C8   16   -0.145  12.0110
> > 17HC1ESV6 H8   170.156   1.0080
> > 18  CAro1ESV6C10   18   -0.360  12.0110
> > 19HC1ESV6 H9   190.169   1.0080
> > 20 C1ESV6 C3   20   -0.159  12.0110
> > 21HC1ESV6 H1   210.070   1.0080
> > 22HC1ESV6 H2   220.070   1.0080
> > 23  CPos1ESV6 C6   230.231  12.0110
> > 24HC1ESV6 H4   240.014   1.0080
> > 25HC1ESV6 H5   250.014   1.0080
> > 26 N1ESV6 N2   26   -0.525  14.0067
> > 27  HS141ESV6H10   270.307   1.0080
> > 28  CPos1ESV6C11   280.684  12.0110
> > 29 OEOpt1ESV6 O2   29   -0.616  15.9994
> > 30 C1ESV6C12   30   -0.586  12.0110
> > 31HC1ESV6H11   310.166   1.0080
> > 32HC1ESV6H12   320.166   1.0080
> > 33HC1ESV6H13   330.166   1.0080
> > ; total charge of the molecule:   0.000
> > [ bonds ]
> > ;  ai   aj  funct   c0 c1
> >  122   0.1090   1.2300e+07
> >  232   0.1090   1.2300e+07
> >  242   0.1090   1.2300e+07
> >  252   0.1430   8.1800e+06
> >  562   0.1380   4.4633e+06
> >  672   0.1390   8.6600e+06
> >  6   182   0.1420   3.2236e+06
> >  782   0.1090   1.2300e+07
> >  792   0.1410   6.5389e+06
> >  9   102   0.1435   6.1000e+06
> >  9   152   0.1430   8.1800e+06
> > 10   112   0.1380   1.1000e+07
> > 10   202   0.1500   8.3700e+06
> > 11   122   0.1090   1.2300e+07
> > 11   132   0.1380   1.1000e+07
> > 13   142   0.1010   6.3719e+06
> > 13   152   0.1380   1.1000e+07
> > 15   162   0.1400   8.5400e+06
> > 16   172   0.1090   1.2300e+07
> > 16   182   0.1390   8.6600e+06
> > 18   192   0.1090   1.2300e+07
> > 20   212   0.1090   1.2300e+07
> > 20   22

[gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

[Du, Yu]

Dear GMX-Users, 

I'm using GMX2018.3 simulating Melatonin (ATB Link: 
https://atb.uq.edu.au/molecule.py?molid=355098).


I found that the hydrogens of two methyl groups (CH3, i.e. CH11, CH12, CH13, 
CH14, CH15 and CH16) showed 
obvious vibration under the following mdp configuration:


integrator  = md
dt   = 0.002
cutoff-scheme= group
constraints = all-bonds
constraint_algorithm = lincs
continuation  = yes


I used the gromos54a7_atb.ff. 




P.S. The partial topology of Melatonin from ATB 
[ moleculetype ]
; Name   nrexcl
ESV6 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
1HC1ESV6H1610.067   1.0080
2  CPos1ESV6C1320.010  12.0110
3HC1ESV6H1430.067   1.0080
4HC1ESV6H1540.067   1.0080
5OE1ESV6 O15   -0.368  15.9994
6  CAro1ESV6 C960.398  12.0110
7  CAro1ESV6 C77   -0.385  12.0110
8HC1ESV6 H780.163   1.0080
9  CAro1ESV6 C290.085  12.0110
   10  CAro1ESV6 C1   10   -0.057  12.0110
   11  CAro1ESV6 C5   11   -0.144  12.0110
   12HC1ESV6 H3   120.186   1.0080
   13  NOpt1ESV6 N1   13   -0.354  14.0067
   14  HS141ESV6 H6   140.373   1.0080
   15  CAro1ESV6 C4   150.070  12.0110
   16  CAro1ESV6 C8   16   -0.145  12.0110
   17HC1ESV6 H8   170.156   1.0080
   18  CAro1ESV6C10   18   -0.360  12.0110
   19HC1ESV6 H9   190.169   1.0080
   20 C1ESV6 C3   20   -0.159  12.0110
   21HC1ESV6 H1   210.070   1.0080
   22HC1ESV6 H2   220.070   1.0080
   23  CPos1ESV6 C6   230.231  12.0110
   24HC1ESV6 H4   240.014   1.0080
   25HC1ESV6 H5   250.014   1.0080
   26 N1ESV6 N2   26   -0.525  14.0067
   27  HS141ESV6H10   270.307   1.0080
   28  CPos1ESV6C11   280.684  12.0110
   29 OEOpt1ESV6 O2   29   -0.616  15.9994
   30 C1ESV6C12   30   -0.586  12.0110
   31HC1ESV6H11   310.166   1.0080
   32HC1ESV6H12   320.166   1.0080
   33HC1ESV6H13   330.166   1.0080
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
122   0.1090   1.2300e+07
232   0.1090   1.2300e+07
242   0.1090   1.2300e+07
252   0.1430   8.1800e+06
562   0.1380   4.4633e+06
672   0.1390   8.6600e+06
6   182   0.1420   3.2236e+06
782   0.1090   1.2300e+07
792   0.1410   6.5389e+06
9   102   0.1435   6.1000e+06
9   152   0.1430   8.1800e+06
   10   112   0.1380   1.1000e+07
   10   202   0.1500   8.3700e+06
   11   122   0.1090   1.2300e+07
   11   132   0.1380   1.1000e+07
   13   142   0.1010   6.3719e+06
   13   152   0.1380   1.1000e+07
   15   162   0.1400   8.5400e+06
   16   172   0.1090   1.2300e+07
   16   182   0.1390   8.6600e+06
   18   192   0.1090   1.2300e+07
   20   212   0.1090   1.2300e+07
   20   222   0.1090   1.2300e+07
   20   232   0.1540   4.0057e+06
   23   242   0.1090   1.2300e+07
   23   252   0.1090   1.2300e+07
   23   262   0.1460   4.6913e+06
   26   272   0.1010   6.3719e+06
   26   282   0.1360   1.0200e+07
   28   292   0.1230   1.6600e+07
   28   302   0.1520   5.4300e+06
   30   312   0.1090   1.2300e+07
   30   322   0.1090   1.2300e+07
   30   332   0.1090   1.2300e+07




--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
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Re: [gmx-users] Gromacs 2018.3 install warning

[Du, Yu]

All right. Thanks for reply.

At2018-08-29 20:04:49,Paul bauerwrote:
> Hello,
> 
> we have not yet full support for gcc-8, but this is being worked on. You 
> can disregard those warnings safely for now.
> 
> /Paul
> 
> On 29/08/2018 14:01, Du, Yu wrote:
> > Dear gmx-users,
> >
> >
> >
> >
> > I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the 
> > following warning:
> >
> >
> > `make check` with regression test set 100% passed. Hope next version will 
> > fix these warnings.
> >
> >
> > ##Warnings##
> > [ 33%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:
> >  In function ‘void make_benchmark_tprs(const char*, char**, gmx_int64_t, 
> > gmx_int64_t, real, real, real, int*, t_inputinfo*, FILE*)’:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:21:
> >  warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 
> > depends on the length of the source argument [-Wstringop-overflow=]
> >   std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
> > std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
> >   
> > ^~~
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:63:
> >  note: length computed here
> >   std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
> > std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
> >  ~~~^~~~
> > [ 33%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o
> >
> >
> > [ 35%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o
> > In function ‘void calc_cumulatives(t_UmbrellaWindow*, int, 
> > t_UmbrellaOptions*, const char*, const char*)’,
> >  inlined from ‘void do_bootstrapping(const char*, const char*, const 
> > char*, const char*, char*, double*, t_UmbrellaWindow*, int, 
> > t_UmbrellaOptions*)’ at 
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1689:29:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:16:
> >  warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 
> > depends on the length of the source argument [-Wstringop-overflow=]
> >   sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4));
> >   
> > ~~~^~
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
> >  In function ‘void do_bootstrapping(const char*, const char*, const char*, 
> > const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:74:
> >  note: length computed here
> >   sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4));
> > 
> > ~~~^~~~
> > In function ‘void print_histograms(const char*, t_UmbrellaWindow*, int, 
> > int, t_UmbrellaOptions*, const char*)’,
> >  inlined from ‘void do_bootstrapping(const char*, const char*, const 
> > char*, const char*, char*, double*, t_UmbrellaWindow*, int, 
> > t_UmbrellaOptions*)’ at 
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1735:29:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:16:
> >  warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 
> > depends on the length of the source argument [-Wstringop-overflow=]
> >   sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4), bs_index);
> >   
> > ~~~^~~
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
> >  In function ‘void do_bootstrapping(const char*, const char*, const char*, 
> > const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
> > /share/home/para008/software_new/src/gr

[gmx-users] Gromacs 2018.3 install warning

[Du, Yu]

Dear gmx-users,




I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the following 
warning:


`make check` with regression test set 100% passed. Hope next version will fix 
these warnings.


##Warnings##
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:
 In function ‘void make_benchmark_tprs(const char*, char**, gmx_int64_t, 
gmx_int64_t, real, real, real, int*, t_inputinfo*, FILE*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:21:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
 std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
 
^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:63:
 note: length computed here
 std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
~~~^~~~
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o


[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o
In function ‘void calc_cumulatives(t_UmbrellaWindow*, int, t_UmbrellaOptions*, 
const char*, const char*)’,
inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1689:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
 sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));
 
~~~^~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:74:
 note: length computed here
 sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));
   
~~~^~~~
In function ‘void print_histograms(const char*, t_UmbrellaWindow*, int, int, 
t_UmbrellaOptions*, const char*)’,
inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1735:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
 sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
 
~~~^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:73:
 note: length computed here
 sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
  
~~~^~~~
[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o
##Warnings######



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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[gmx-users] how to checkpoint per steps

[Du, Yu]

Dear GMX Users, 


In GMX, I can't checkpoint per some MD steps but only checkpoint per wall time 
period, right?



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] only interaction inside the molecule

[Du, Yu]

Hi Faezeh, 

I got you point. I believe the link and the PDB file in that webpage I 
mentioned previously can help you. You need an index.ndx file that defines the 
specific oxygens in your system and the rest of the system.

The charge, the vdw sigma and epsilon (or c6 and c12) in the top file of your 
CO2 is global parameters, which means that if you change them the interaction 
in a single molecule will also be changed.

Best, 
Yu

> -Original Messages-
> From: "Faezeh Pousaneh" 
> Sent Time: 2017-11-09 17:30:02 (Thursday)
> To: gmx-users 
> Cc: 
> Subject: Re: [gmx-users] only interaction inside the molecule
> 
> no that is not my answer Yu.
> 
> for example I would like to design a molecule e.g. CO2, I would like
> oxygens connected to Carbon in each molecule, but do no interact with rest
> of system.
> I guess I should change the ffbonded.itp in the following:
> 
> keep the length bond but change the interaction strength to zero, and then
> restrain the bond length in .mpd file.
> but I am not sure ?
> 
> 
> 
> Best regards
> 
> 
> On Thu, Nov 9, 2017 at 10:15 AM, Du, Yu  wrote:
> 
> > Hi,
> >
> > From your limited information, I suggest you have a look at the Tabulated
> > Potentials, www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
> >
> > Best,
> > Yu
> >
> > --
> > Du, Yu
> > PhD Student,
> > Shanghai Institute of Organic Chemistry
> > 345 Ling Ling Rd., Shanghai, China.
> > Zip: 200032, Tel: (86) 021 5492 5275
> >
> > > -Original Messages-
> > > From: "Faezeh Pousaneh" 
> > > Sent Time: 2017-11-09 16:58:12 (Thursday)
> > > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > > Cc:
> > > Subject: [gmx-users] only interaction inside the molecule
> > >
> > > Hi,
> > >
> > > I would like an atom of my molecule only interact (LJ) with its own
> > > molecule, not the rest of system, how can I do that?
> > >
> > > thanks for reply,
> > > Best regards


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Re: [gmx-users] only interaction inside the molecule

[Du, Yu]

Hi, 

>From your limited information, I suggest you have a look at the Tabulated 
>Potentials, www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

Best,
Yu

--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

> -Original Messages-
> From: "Faezeh Pousaneh" 
> Sent Time: 2017-11-09 16:58:12 (Thursday)
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc: 
> Subject: [gmx-users] only interaction inside the molecule
> 
> Hi,
> 
> I would like an atom of my molecule only interact (LJ) with its own
> molecule, not the rest of system, how can I do that?
> 
> thanks for reply,
> Best regards



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Re: [gmx-users] Determining a ligands permeability

[Du, Yu]

> On 11/6/17 12:22 AM, Du, Yu wrote:
> > Hi, Justin,
> >
> > Thanks for your question. Presume that ligands were in only one side of the 
> > box outside of the membrane.
> >
> > 1)In metadynamics, the membrane will be pushed by the ligands. After long 
> > time simulation, the membrane may move along the Z-axis.
> >
> > 2)In steer MD, one ligand will be pulled across the membrane and the 
> > membrane can also moves along the Z-axis.
> >
> > This is the reason that I said some POSRES should be applied on the Z-axis 
> > of the lipids.
> >
> > So, what is your opinion, Justin?
> 
> I disagree. Who cares if the lipids move? The reaction coordinate is the 
> relative distance between the ligand and membrane COM. In a periodic 
> system, the "center" is arbitrary as is the "sidedness" of the system 
> you propose.
> 
> If you restrain the lipids, you perturb their dynamics and likely 
> influence the free energy of permeation across the membrane. It's not 
> wise. A sufficiently slow/gentle pull across the membrane should not 
> significantly perturb the membrane in any detrimental way. I've seen 
> this done many times.
> 
> -Justin
> 

Thanks, Justin. I accept your convincing viewpoint that there shouldn't be any 
POSRES in the system.

Yu
--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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Re: [gmx-users] Determining a ligands permeability

[Du, Yu]

Hi, Justin, 

Thanks for your question. Presume that ligands were in only one side of the box 
outside of the membrane. 

1)In metadynamics, the membrane will be pushed by the ligands. After long time 
simulation, the membrane may move along the Z-axis.

2)In steer MD, one ligand will be pulled across the membrane and the membrane 
can also moves along the Z-axis.

This is the reason that I said some POSRES should be applied on the Z-axis of 
the lipids.

So, what is your opinion, Justin?

Regards, 
Yu


> -Original Messages-
> From: "Justin Lemkul" 
> Sent Time: 2017-11-06 01:14:22 (Monday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Determining a ligands permeability
> 
> 
> 
> On 11/5/17 7:40 AM, Du, Yu wrote:
> > Hi,
> >
> > I don't study the membrane permeability of small molecules and can't give 
> > related papers.
> >
> > All in all, you need to first successfully simulate the lipid-small 
> > molecule system and then enhanced sampling because of the time scale of 
> > ligand diffusing across the membrane.
> >
> > There are some approaches to study it, such as, Metadynamics and steer MD.
> >
> > For Metadynamics, you can use the PLUMED with GMX and exercise larger 
> > confining potential if the ligand further away from the membrane in the 
> > water. Then, compare the chance or time that one ligand can penetrate 
> > across the entire or in the half of membrane. You can add excessive ligands 
> > in the water.
> >
> > For steer MD, you can follow Justin's tutorial. In both approaches, lipids 
> > should be under some position restraints.
> 
> Why would the lipids need to be restrained in this case? I would argue 
> the opposite. It's a spurious force in this case.
> 
> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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Re: [gmx-users] Determining a ligands permeability

[Du, Yu]

Hi, 

I don't study the membrane permeability of small molecules and can't give 
related papers.

All in all, you need to first successfully simulate the lipid-small molecule 
system and then enhanced sampling because of the time scale of ligand diffusing 
across the membrane.

There are some approaches to study it, such as, Metadynamics and steer MD.

For Metadynamics, you can use the PLUMED with GMX and exercise larger confining 
potential if the ligand further away from the membrane in the water. Then, 
compare the chance or time that one ligand can penetrate across the entire or 
in the half of membrane. You can add excessive ligands in the water.

For steer MD, you can follow Justin's tutorial. In both approaches, lipids 
should be under some position restraints.

Best, 
Yu

> -Original Messages-
> From: "Chetan Puri" 
> Sent Time: 2017-11-05 19:39:47 (Sunday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: [gmx-users] Determining a ligands permeability
> 
> I have tried to do an umbrella sampling for a ligand (drug) and membrane as
> per the gromacs tutorial. Now i want to calculate permeability and
> diffusibility for this ligand, so can anyone suggest how to proceed further.
> Since there is some literature available but it does not show the proper
> method applied.
> 
> 
> Virus-free.
> www.avast.com
> 
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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Re: [gmx-users] [gmx-developers] Fw: Fw: Two questions about PME-User in coulombtype

[Du, Yu]

Berk, thanks for your reply.

I have Cc this email including your answers to the GMX-User.

Regards, 

Yu

> -Original Messages-
> From: "Berk Hess" 
> Sent Time: 2017-10-18 19:56:30 (Wednesday)
> To: gmx-develop...@gromacs.org
> Cc: 
> Subject: Re: [gmx-developers] Fw: [gmx-users] Fw: Two questions about 
> PME-User in coulombtype
> 
> Hi,
> 
> I don't know if I can still mail to the gmx-users list (and I don't have 
> time to check now), so I answer to the devloper list, but please post my 
> answers below to the gmx-users list.
> 
> Cheers,
> 
> Berk
> 
> Answers:
> 
> 1) Correct.
> 2) Correct.
> 3) PME splits the Coulomb interaction into two parts and this splitting 
> depends on beta. All you need to know is that up to the cut-off 
> distance, you exactly get the interaction you set in the table. Beyond 
> the cut-off you get 1/r.
> 
> Your potential values should have 10 decimals to be sure that rounding 
> errors are negligible. In principle, also r should have 10 decimals, but 
> 0.002000 is identical to 0.002 (and 0.00 to 0.000 or 0).
> 
> On 2017-10-17 15:15, Du, Yu wrote:
> > Dear GMX Developers,
> >
> > I'm sorry for repeting sending this email to the mail list. I think the 
> > PME-User is not common for users to use and the related explanation is 
> > scarce.
> >
> > Hope you gurus can help me. Thanks a lot.
> >
> > Yu
> >
> >
> > -Original Messages-
> > From: "Du, Yu" 
> > Sent Time: 2017-10-15 17:17:14 (Sunday)
> > To: GMX-user 
> > Subject: [gmx-users] Two questions about PME-User in coulombtype
> >
> > Hi GMX Users,
> >
> >
> > I'm using tabulized potentials between energygrp-table = Protein Ligand. 
> > I'm writing to inquiring the details of PME-User parameter.
> >
> >
> > I have seen some discussions in the GMX User mail list and the explanation 
> > in user guide. I still can't ensure I have grasped the meaning of PME-User 
> > in coulombtype option. The following is my understanding. If anything is 
> > wrong please point out. Thanks a lot.
> >
> >
> > 1) Because the mesh part also contributes below the cut-off, the PME mesh 
> > contribution is subtracted from the user table by gmx mdrun to get the 
> > short-range coulombic interaction below the rcoulomb.
> >
> >
> > 2) The tabulized potential is short-range interaction. If I use 
> > coulombtype=User, I only have the short-range interaction defined in the 
> > tabulized potetial files and no PME between any components (i.e. Protein, 
> > Ligand, SOL, ions) in the system.
> >
> >
> > 3)If I use coulombtype=PME-User instead, I will get the short-range 
> > interaction defined in the tabulized potetial files and PME between any 
> > components (i.e. Protein, Ligand, SOL, ions) in the system like normal 
> > coulombtype=PME.
> >
> >
> > --Next Question--
> > "The PME mesh contribution is subtracted from the user table by gmx mdrun. 
> > Because of this subtraction the user tables should contain about 10 decimal 
> > places."
> >
> > The second question is how to deal with the PME-User's "10 decimal places" 
> > in user guide of the coulombtype option. Does it mean that the original 
> > step of r = 0.002 nm in mixed precision should be 0.0# nm? What 
> > should be the detailed step size of r?
> >
> >
> >
> 

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[gmx-users] Fw: Two questions about PME-User in coulombtype

[Du, Yu]

Dear Hess, 

I have two questions about the usage of the PME-User in coulombtype parameter.
I didn't get replies from the GMX-USER mail list. Could you please give some 
details? The forwarded mail is the two questions I asked.

Thanks for your help.

Yu

-Original Messages-
From: "Du, Yu" 
Sent Time: 2017-10-15 17:17:14 (Sunday)
To: GMX-user 
Subject: [gmx-users] Two questions about PME-User in coulombtype

Hi GMX Users, 


I'm using tabulized potentials between energygrp-table = Protein Ligand. I'm 
writing to inquiring the details of PME-User parameter.


I have seen some discussions in the GMX User mail list and the explanation in 
user guide. I still can't ensure I have grasped the meaning of PME-User in 
coulombtype option. The following is my understanding. If anything is wrong 
please point out. Thanks a lot.


1) Because the mesh part also contributes below the cut-off, the PME mesh 
contribution is subtracted from the user table by gmx mdrun to get the 
short-range coulombic interaction below the rcoulomb.


2) The tabulized potential is short-range interaction. If I use 
coulombtype=User, I only have the short-range interaction defined in the 
tabulized potetial files and no PME between any components (i.e. Protein, 
Ligand, SOL, ions) in the system.


3)If I use coulombtype=PME-User instead, I will get the short-range interaction 
defined in the tabulized potetial files and PME between any components (i.e. 
Protein, Ligand, SOL, ions) in the system like normal coulombtype=PME.


--Next Question--
"The PME mesh contribution is subtracted from the user table by gmx mdrun. 
Because of this subtraction the user tables should contain about 10 decimal 
places."
The second question is how to deal with the PME-User's "10 decimal places" in 
user guide of the coulombtype option. Does it mean that the original step of r 
= 0.002 nm in mixed precision should be 0.0# nm? What should be the 
detailed step size of r?



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

-- 
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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[gmx-users] Two questions about PME-User in coulombtype

[Du, Yu]

Hi GMX Users, 


I'm using tabulized potentials between energygrp-table = Protein Ligand. I'm 
writing to inquiring the details of PME-User parameter.


I have seen some discussions in the GMX User mail list and the explanation in 
user guide. I still can't ensure I have grasped the meaning of PME-User in 
coulombtype option. The following is my understanding. If anything is wrong 
please point out. Thanks a lot.


1) Because the mesh part also contributes below the cut-off, the PME mesh 
contribution is subtracted from the user table by gmx mdrun to get the 
short-range coulombic interaction below the rcoulomb.


2) The tabulized potential is short-range interaction. If I use 
coulombtype=User, I only have the short-range interaction defined in the 
tabulized potetial files and no PME between any components (i.e. Protein, 
Ligand, SOL, ions) in the system.


3)If I use coulombtype=PME-User instead, I will get the short-range interaction 
defined in the tabulized potetial files and PME between any components (i.e. 
Protein, Ligand, SOL, ions) in the system like normal coulombtype=PME.


--Next Question--
"The PME mesh contribution is subtracted from the user table by gmx mdrun. 
Because of this subtraction the user tables should contain about 10 decimal 
places."
The second question is how to deal with the PME-User's "10 decimal places" in 
user guide of the coulombtype option. Does it mean that the original step of r 
= 0.002 nm in mixed precision should be 0.0# nm? What should be the 
detailed step size of r?




--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
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
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Duplicate lipid bilayer, simulate protein and remove extra lipid bilayer

[Du, Yu]

Dear GMX Users, 


My question is 512-lipid bilayer is too big. How can I resize it and the 
cooresponding box size?


I duplicated the 128-lipid bilayer using 
$gmx_mpi genconf -f lipid128.gro -o lipid_new.gro -nbox 2 2 1


But the new 512-lipid bilayer is so large, I want to remove the some lipids 
according to the x and y coordinate.


I know the parameter -nbox uses integers. But is there any easy way to fulfill 
the function like `gmx_mpi genconf -f lipid128.gro -o lipid_new.gro -nbox 1.5 
1.5 1`?


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
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
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Re: [gmx-users] Fw: Potassium channel EM Segmentation fault

[Du, Yu]

Thanks for Mark's prompt reply.

I find there indeed are overlapping potassiums from each chain and I remove the 
extra potassiums then EM succeeds.

Yu


> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: 2017-10-11 22:12:29 (Wednesday)
> To: gmx-us...@gromacs.org, GMX-user 
> 
> Cc: 
> Subject: Re: [gmx-users] Fw: Potassium channel EM Segmentation fault
> 
> Hi,
> 
> This is probably a case of
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up and I suggest
> you consider some of the investigation approaches documented there.
> 
> Mark
> 
> On Wed, Oct 11, 2017 at 4:07 PM Du, Yu  wrote:
> 
> >
> >
> >
> > -Original Messages-
> > From:"Du, Yu" 
> > Sent Time:2017-10-11 21:55:38 (Wednesday)
> > To: GMX-user 
> > Cc:
> > Subject: Potassium channel EM Segmentation fault
> >
> > Dear GMX Users,
> >
> >
> > Keyword: metal, energy minimization, segmentation fault
> >
> >
> > I have pinpointed the source of EM error. EM succeeds only without
> > potassiums.
> >
> >
> > I used PDB 1r3j and changed the TL to K.
> > You can download the my 1r3j here and reproduce the error like this.
> >
> >
> > $gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p
> > $gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr
> > $mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr
> >
> >
> > Thanks for any solutions.
> >
> >
> > ##The minim.mdp file##
> > define=-DPOSRES
> > ; Parameters describing what to do, when to stop and what to save
> > integrator  = steep ; Algorithm (steep = steepest descent minimization)
> > emtol   = 1000.0; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep  = 0.01  ; Energy step size
> > nsteps  = 5 ; Maximum number of (minimization) steps to perform
> >
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist = 1 ; Frequency to update the neighbor list and long
> > range forces
> > cutoff-scheme = verlet
> > ns_type = grid  ; Method to determine neighbor list (simple, grid)
> > rlist   = 1.2   ; Cut-off for making neighbor list (short range
> > forces)
> > coulombtype = PME   ; Treatment of long range electrostatic
> > interactions
> > rcoulomb= 1.2   ; Short-range electrostatic cut-off
> > rvdw= 1.2   ; Short-range Van der Waals cut-off
> > pbc = xyz   ; Periodic Boundary Conditions
> > ###END##
> >
> >
> > EM Error
> >
> > Steepest Descents:
> >Tolerance (Fmax)   =  1.0e+03
> >Number of steps=5
> > [gpu-new:22930] *** Process received signal ***
> > [gpu-new:22930] Signal: Segmentation fault (11)
> > [gpu-new:22930] Signal code: Address not mapped (1)
> > [gpu-new:22930] Failing at address: 0xfffe01bf6dd0
> > [gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710]
> > [gpu-new:22930] [ 1]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f]
> > [gpu-new:22930] [ 2]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f]
> > [gpu-new:22930] [ 3]
> > /home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf]
> > [gpu-new:22930] [ 4]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd]
> > [gpu-new:22930] [ 5]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7]
> > [gpu-new:22930] [ 6]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d]
> > [gpu-new:22930] [ 7]
> > /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3]
> > [gpu-new:22930] [ 8]
> > gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliifffim+0x190a)[0x4101ca]
> > [g

[gmx-users] Fw: Potassium channel EM Segmentation fault

[Du, Yu]

-Original Messages-
From:"Du, Yu" 
Sent Time:2017-10-11 21:55:38 (Wednesday)
To: GMX-user 
Cc:
Subject: Potassium channel EM Segmentation fault

Dear GMX Users, 


Keyword: metal, energy minimization, segmentation fault 


I have pinpointed the source of EM error. EM succeeds only without potassiums. 


I used PDB 1r3j and changed the TL to K.
You can download the my 1r3j here and reproduce the error like this.


$gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p
$gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr
$mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr


Thanks for any solutions.


##The minim.mdp file##
define=-DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform


; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme = verlet
ns_type = grid  ; Method to determine neighbor list (simple, grid)
rlist   = 1.2   ; Cut-off for making neighbor list (short range forces)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
###END##


EM Error

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
[gpu-new:22930] *** Process received signal ***
[gpu-new:22930] Signal: Segmentation fault (11)
[gpu-new:22930] Signal code: Address not mapped (1)
[gpu-new:22930] Failing at address: 0xfffe01bf6dd0
[gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710]
[gpu-new:22930] [ 1] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f]
[gpu-new:22930] [ 2] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f]
[gpu-new:22930] [ 3] 
/home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf]
[gpu-new:22930] [ 4] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd]
[gpu-new:22930] [ 5] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7]
[gpu-new:22930] [ 6] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d]
[gpu-new:22930] [ 7] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3]
[gpu-new:22930] [ 8] 
gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliifffim+0x190a)[0x4101ca]
[gpu-new:22930] [ 9] gmx_mpi(_Z9gmx_mdruniPPc+0x1766)[0x421516]
[gpu-new:22930] [10] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2a3)[0x2b19661a5693]
[gpu-new:22930] [11] gmx_mpi(main+0x7c)[0x40cd3c]
[gpu-new:22930] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x383621ed1d]
[gpu-new:22930] [13] gmx_mpi[0x40cb79]
[gpu-new:22930] *** End of error message ***
--
mpirun noticed that process rank 0 with PID 0 on node gpu-new exited on signal 
11 (Segmentation fault).
--
###END##########


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
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.

[gmx-users] Potassium channel EM Segmentation fault

[Du, Yu]

Dear GMX Users, 


Keyword: metal, energy minimization, segmentation fault 


I have pinpointed the source of EM error. EM succeeds only without potassiums. 


I used PDB 1r3j and changed the TL to K.
You can download the my 1r3j here and reproduce the error like this.


$gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p
$gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr
$mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr


Thanks for any solutions.


##The minim.mdp file##
define=-DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform


; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme = verlet
ns_type = grid  ; Method to determine neighbor list (simple, grid)
rlist   = 1.2   ; Cut-off for making neighbor list (short range forces)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
###END##


EM Error

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
[gpu-new:22930] *** Process received signal ***
[gpu-new:22930] Signal: Segmentation fault (11)
[gpu-new:22930] Signal code: Address not mapped (1)
[gpu-new:22930] Failing at address: 0xfffe01bf6dd0
[gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710]
[gpu-new:22930] [ 1] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f]
[gpu-new:22930] [ 2] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f]
[gpu-new:22930] [ 3] 
/home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf]
[gpu-new:22930] [ 4] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd]
[gpu-new:22930] [ 5] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7]
[gpu-new:22930] [ 6] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d]
[gpu-new:22930] [ 7] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3]
[gpu-new:22930] [ 8] 
gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliifffim+0x190a)[0x4101ca]
[gpu-new:22930] [ 9] gmx_mpi(_Z9gmx_mdruniPPc+0x1766)[0x421516]
[gpu-new:22930] [10] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2a3)[0x2b19661a5693]
[gpu-new:22930] [11] gmx_mpi(main+0x7c)[0x40cd3c]
[gpu-new:22930] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x383621ed1d]
[gpu-new:22930] [13] gmx_mpi[0x40cb79]
[gpu-new:22930] *** End of error message ***
--
mpirun noticed that process rank 0 with PID 0 on node gpu-new exited on signal 
11 (Segmentation fault).
--
###END##


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
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
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] CLOSED and DUPLICATED Re: Elegent way to continue md or trjcat continue trajectory

[Du, Yu]

Similar question has been answered by the following link:
http://thread.gmane.org/gmane.science.biology.gromacs.user/72772

The tinit option in .mdp file, which sets the starting time for continuous MD 
run.

If I use tinit in .mdp file, the second question will not exist. 

Yu


> -Original Messages-
> From: "Du, Yu" 
> Sent Time: 2017-09-29 12:12:00 (Friday)
> To: GMX-user 
> Cc: 
> Subject: [gmx-users] Elegent way to continue md or trjcat continue trajectory
> 
> Dear GMX Users, 
> 
> 
> I run MD after the previous MD and want to concatenate trajectories from 
> these N continuous MDs.
> 
> 
> 1) Do I need special time setting for the second MD to avoid the trjcat 
> confusing time setting?
> OR 2) Is there any ways to avoid the verbose interactive -setime, which needs 
> the N "c" input? 
> 
> Thanks.
> 
> 
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China. 
> Zip: 200032, Tel: (86) 021 5492 5275
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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[gmx-users] Elegent way to continue md or trjcat continue trajectory

[Du, Yu]

Dear GMX Users, 


I run MD after the previous MD and want to concatenate trajectories from these 
N continuous MDs.


1) Do I need special time setting for the second MD to avoid the trjcat 
confusing time setting?
OR 2) Is there any ways to avoid the verbose interactive -setime, which needs 
the N "c" input? 

Thanks.


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] manually adding non-bonded interactions based on atom number to topology file

[Du, Yu]

so seems like this depends on the force field and
> that
> > sometimes [ pairs ] should only be for a list of 1-4 interactions. Since
> > I'm writing my own topology (not using pdb2gmx), what will [ pairs ]
> > specify? Will the parameters in [ pairs ] override the parameters in [
> > atomtypes ]? I have increased the c6 parameter and decreased the c12
> > parameter considerably, and I'm still not seeing any sign of attraction
> > between monomer-monomer interfaces.
> >
> > [ nonbonded_params ] actually seems like the right place, since I've read
> > that the parameters there *will* override the combination rules, but it
> > looks like this section doesn't take atom numbers, but only atom types.
> > Since I want these bonds to be based on site locations, this won't work.
> Is
> > there a way to specify non-bonded parameters using atom numbers?
> >
> > Any clarification you can provide will be helpful.
> >
> 
> Before delving into this too much, to clarify: you want to simulate a
> polymer melt with some modified interactions between the ends of each
> polymer?
> 
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
> 
> 
> 
> Hi,
> 
> First, You must need a very long simulation box because one monomer's
> length exceed the cut-off.
> 
> I don't think only LJ can naturely make monomers linear polymer. I know you
> need acceleration of one monomer's A end binding to the other's B end. So I
> will recommend the PLUMED to add some far-large-near-small restraints
> between A and B end of different monomers.
> 
> Cheers,
> Yu
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] protein ligand faraway from one another

[Du, Yu]

> -Original Messages-
> From: "Fakhar Alam" 
> Sent Time: 2017-09-28 16:07:52 (Thursday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: [gmx-users] protein ligand faraway from one another
> 
> Dear Gromacs Experts,
> 
> I am doing simulation of protein-ligand complex. However when I follow the
> steps in the tutorial, the ligand is very faraway from the protein. How can
> I put the ligand close to the protein ?
> 
> Thanks,
> Alam
> -- 
> Gromacs Users mailing list
> 
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Before simulation, the protein and ligand is a complex, right?

Can you give the detail of which tutorial you are following and which step have 
you followed to?
Do you follow the tutorial exactly or tune some factors that can impact the 
interaction between protein and ligand?
I have never encountered the problem. We need more information to answer your 
question.

--
Yu
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Re: [gmx-users] manually adding non-bonded interactions based on atom number to topology file

[Du, Yu]

Hi, 

First, You must need a very long simulation box because one monomer's length 
exceed the cut-off.

I don't think only LJ can naturely make monomers linear polymer. I know you 
need acceleration of one monomer's A end binding to the other's B end. So I 
will recommend the PLUMED to add some far-large-near-small restraints between A 
and B end of different monomers.

Cheers, 
Yu

At2017-09-28 08:07:54,Amanda Parkerwrote:
> ​Hello,
> 
> I am trying to create my own topology file in order to simulate assembly of
> a number of identical monomers. I have been reading the manual, mailing
> list, and other online sources, about what all the sections in the topology
> mean and how to construct them, but I'm still confused about what is
> necessary and what overrides what.
> 
> I would like to be able to have any number of monomers in my system and
> therefore I want all the intermolecular interactions to be non-specific. I
> want each monomer to have atom numbers running from 1 to last_atom_number,
> so that I can have atom 1 paired with atom last_atom_number, and see
> binding between any monomer's atom 1 with any other monomer's atom
> last_atom_number.
> 
> So my idea is to create a single topology file, which will contain the
> intramolecular interactions for a single monomer, as well as the
> interactions between atom 1 and atom last_atom_number. The latter will
> probably be Lennard-Jones interactions, since that way the "beginning" of
> one monomer will not interact with its own "end" (due to the cut-off), but
> with other monomers' ends if they get close enough. I'd like to manually
> adjust the parameters for these interactions, to accelerate binding.
> 
> The problem is that I don't know where to put these Lennard Jones
> interactions.
> 
> Right now I have them in the [ pairs ] section, since my understanding is
> that this is where one can put "extra" non-bonded interactions with special
> parameters. But it also seems like this depends on the force field and that
> sometimes [ pairs ] should only be for a list of 1-4 interactions. Since
> I'm writing my own topology (not using pdb2gmx), what will [ pairs ]
> specify? Will the parameters in [ pairs ] override the parameters in [
> atomtypes ]? I have increased the c6 parameter and decreased the c12
> parameter considerably, and I'm still not seeing any sign of attraction
> between monomer-monomer interfaces.
> 
> [ nonbonded_params ] actually seems like the right place, since I've read
> that the parameters there *will* override the combination rules, but it
> looks like this section doesn't take atom numbers, but only atom types.
> Since I want these bonds to be based on site locations, this won't work. Is
> there a way to specify non-bonded parameters using atom numbers?
> 
> Any clarification you can provide will be helpful.
> 
> Thanks,​
> Amanda
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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Re: [gmx-users] Group NS scheme parameter for 2016.3 version

[Du, Yu]

Hi, 


> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: 2017-09-26 21:54:54 (Tuesday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> 
> Hi,
> 
> On Tue, Sep 26, 2017 at 3:38 PM Du, Yu  wrote:
> 
> > Thank Mark's reply.
> >
> > > -Original Messages-
> > > From: "Mark Abraham" 
> > > Sent Time: 2017-09-26 19:44:41 (Tuesday)
> > > To: gmx-us...@gromacs.org
> > > Cc:
> > > Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> > >
> > > Hi,
> > >
> > > On Tue, Sep 26, 2017 at 4:02 AM Du, Yu  wrote:
> > >
> > > > > -Original Messages-
> > > > > From: "Mark Abraham" 
> > > > > Sent Time: 2017-09-26 06:38:40 (Tuesday)
> > > > > To: "Discussion list for GROMACS users" ,
> > > > "Discussion list for GROMACS users" <
> > > > gromacs.org_gmx-users@maillist.sys.kth.se>
> > > > > Cc:
> > > > > Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> > > > >
> > > > > Hi,
> > > > >
> > > > > On Mon, 25 Sep 2017 14:11 Du, Yu  wrote:
> > > > >
> > > > > > Dear GMX Users,
> > > > > >
> > > > > >
> > > > > > Indeed making tabulized potential between groups with Verlet is not
> > > > > > trivial as also discussed in OpenMM issue #1765.
> > > > > >
> > > > > > I'm using gmx 2016.3. If I want use the group NS scheme as precise
> > as
> > > > > > possible, what parameters in mdp file should I set and what are
> > their
> > > > > > recommended values for protein and ligand system.
> > > > > >
> > > > >
> > > > > It's straightforward to implement a tabulated interaction kernel, but
> > > > > rather less clear how best to let the user describe to mdrun how they
> > > > want
> > > > > the calculation to work, eg whether interaction types should be
> > governed
> > > > by
> > > > > atom numbers, or types, or names, and how that should be expressed
> > in the
> > > > > topology. Suggestions for problem types people want to be able to
> > handle
> > > > > are most welcome.
> > > > >
> > > >
> > > > I want to decompose the interaction between protein and ligand, and
> > only
> > > > between them, not others.
> > > > So I think "vdwtype=user, energygrps = Protein Ligand, energygrp-table
> > =
> > > > Protein Ligand and table.xvg table_Protein_ligand.xvg" is the only
> > solution
> > > > in gromacs to achieve it.
> > > >
> > >
> > > Yes. So in future, some method that would select the regions to use the
> > > different tabulated interactions based on atom number (ie index groups)
> > > would work for you.
> >
> > Today I experimented on the tabulated potential with group cut-off scheme.
> > I used custom potential (no coulomb and no attractive vdw) between protein
> > and ligand. I guess it worked. Could you please have a look at the md.log
> > and md.mdp file? and help me assure that there is no question.
> > --md.log---
> > Table routines are used for coulomb: true
> > Table routines are used for vdw: true
> > Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
> > Long Range LJ corr.:  3.4946e-04
> > System total charge: -0.000
> > Read user tables from md_0_3.xvg with 1001 data points.
> > Tabscale = 500 points/nm
> > Read user tables from md_0_3_Protein_MEL.xvg with 1001 data points.
> > Tabscale = 500 points/nm
> > Read user tables from md_0_3.xvg with 1001 data points.
> > Tabscale = 500 points/nm
> > Read user tables from md_0_3.xvg with 1001 data points.
> > Tabscale = 500 points/nm
> > ...
> > Statistics over 11 steps using 1001 frames
> >
> >Energies (kJ/mol)
> >Bond  AngleProper Dih.  Improper Dih.  LJ-14
> > 4.09718e+031.11493e+041.26265e+048.33816e+024.52508e+03
> >  Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)  Potential
> > 4.81316e+044.01305e+04   -2.28798e+03   -4.91463e+05   -3.72257e+05

Re: [gmx-users] Group NS scheme parameter for 2016.3 version

[Du, Yu]

Thank Mark's reply.

> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: 2017-09-26 19:44:41 (Tuesday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> 
> Hi,
> 
> On Tue, Sep 26, 2017 at 4:02 AM Du, Yu  wrote:
> 
> > > -Original Messages-
> > > From: "Mark Abraham" 
> > > Sent Time: 2017-09-26 06:38:40 (Tuesday)
> > > To: "Discussion list for GROMACS users" ,
> > "Discussion list for GROMACS users" <
> > gromacs.org_gmx-users@maillist.sys.kth.se>
> > > Cc:
> > > Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> > >
> > > Hi,
> > >
> > > On Mon, 25 Sep 2017 14:11 Du, Yu  wrote:
> > >
> > > > Dear GMX Users,
> > > >
> > > >
> > > > Indeed making tabulized potential between groups with Verlet is not
> > > > trivial as also discussed in OpenMM issue #1765.
> > > >
> > > > I'm using gmx 2016.3. If I want use the group NS scheme as precise as
> > > > possible, what parameters in mdp file should I set and what are their
> > > > recommended values for protein and ligand system.
> > > >
> > >
> > > It's straightforward to implement a tabulated interaction kernel, but
> > > rather less clear how best to let the user describe to mdrun how they
> > want
> > > the calculation to work, eg whether interaction types should be governed
> > by
> > > atom numbers, or types, or names, and how that should be expressed in the
> > > topology. Suggestions for problem types people want to be able to handle
> > > are most welcome.
> > >
> >
> > I want to decompose the interaction between protein and ligand, and only
> > between them, not others.
> > So I think "vdwtype=user, energygrps = Protein Ligand, energygrp-table =
> > Protein Ligand and table.xvg table_Protein_ligand.xvg" is the only solution
> > in gromacs to achieve it.
> >
> 
> Yes. So in future, some method that would select the regions to use the
> different tabulated interactions based on atom number (ie index groups)
> would work for you.

Today I experimented on the tabulated potential with group cut-off scheme. I 
used custom potential (no coulomb and no attractive vdw) between protein and 
ligand. I guess it worked. Could you please have a look at the md.log  and 
md.mdp file? and help me assure that there is no question.
--md.log---
Table routines are used for coulomb: true
Table routines are used for vdw: true
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
Long Range LJ corr.:  3.4946e-04
System total charge: -0.000
Read user tables from md_0_3.xvg with 1001 data points.
Tabscale = 500 points/nm
Read user tables from md_0_3_Protein_MEL.xvg with 1001 data points.
Tabscale = 500 points/nm
Read user tables from md_0_3.xvg with 1001 data points.
Tabscale = 500 points/nm
Read user tables from md_0_3.xvg with 1001 data points.
Tabscale = 500 points/nm
...
Statistics over 11 steps using 1001 frames

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
4.09718e+031.11493e+041.26265e+048.33816e+024.52508e+03
 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)  Potential
4.81316e+044.01305e+04   -2.28798e+03   -4.91463e+05   -3.72257e+05
Kinetic En.   Total Energy  Conserved En.Temperature Pres. DC (bar)
8.98371e+04   -2.82420e+052.61416e+063.37891e+02   -2.51191e+02
 Pressure (bar)   Constr. rmsd
5.71728e+020.0e+00

   Total Virial (kJ/mol)
2.46727e+041.69577e+015.39006e+01
1.69965e+012.48000e+04   -4.34063e+01
5.38208e+01   -4.28545e+012.47416e+04

   Pressure (bar)
5.78692e+02   -5.85172e+00   -3.91771e+00
   -5.85597e+005.67516e+027.54656e+00
   -3.90895e+007.48597e+005.68976e+02

  Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14   
Protein-Protein   -8.49851e+04   -8.95750e+034.83260e+044.44865e+03
Protein-MEL0.0e+001.57386e+010.0e+000.0e+00
   Protein-rest   -3.16047e+04   -1.50902e+030.0e+000.0e+00
MEL-MEL   -3.28886e+02   -2.02938e+01   -1.94359e+027.64322e+01
   MEL-rest   -1.16305e+03   -6.90968e+010.0e+000.0e+00
  rest-rest   -3.73381e+055.06707e+040.0e+000.0e+00

T-MEL_NA_Protein   T-SOL_CL
3.41647e+023.37007e+02
--md.log---
--md.mdp-

Re: [gmx-users] Group NS scheme parameter for 2016.3 version

[Du, Yu]

> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: 2017-09-26 06:38:40 (Tuesday)
> To: "Discussion list for GROMACS users" , "Discussion 
> list for GROMACS users" 
> Cc: 
> Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> 
> Hi,
> 
> On Mon, 25 Sep 2017 14:11 Du, Yu  wrote:
> 
> > Dear GMX Users,
> >
> >
> > Indeed making tabulized potential between groups with Verlet is not
> > trivial as also discussed in OpenMM issue #1765.
> >
> > I'm using gmx 2016.3. If I want use the group NS scheme as precise as
> > possible, what parameters in mdp file should I set and what are their
> > recommended values for protein and ligand system.
> >
> 
> It's straightforward to implement a tabulated interaction kernel, but
> rather less clear how best to let the user describe to mdrun how they want
> the calculation to work, eg whether interaction types should be governed by
> atom numbers, or types, or names, and how that should be expressed in the
> topology. Suggestions for problem types people want to be able to handle
> are most welcome.
> 

I want to decompose the interaction between protein and ligand, and only 
between them, not others.
So I think "vdwtype=user, energygrps = Protein Ligand, energygrp-table = 
Protein Ligand and table.xvg table_Protein_ligand.xvg" is the only solution in 
gromacs to achieve it.

> How to set up the nonbonded scheme for a given force field varies with the
> force field, either based on how it was parameterized or been shown to work
> in practice. This is standard practice. A major defect of the group scheme
> is that it is inefficient with a buffered list, but that is your tradeoff
> to make.
> 

Yes, this is my major confusion. Amber FF don't use charge group not like 
GROMOS FF. I need to work with Amber FF, so is it proper to use amber99sb-ildn 
and gaff with group cut-off scheme?

And now the manual and user guide is dominated by Verlet cut-off scheme, where 
can I find the guide of using group cut-off scheme? I can't tell which options 
is for group scheme in the Molecular dynamics parameters (.mdp).

The following is what I found in 
regressiontests-2016.3/kernel/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4/grompp.mdp
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
cutoff-scheme= Group
; nblist update frequency
nstlist  = 1
; ns algorithm (simple or grid)
ns-type  = Grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic-molecules   = no
; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-drift  = 0.005
; nblist cut-off
rlist= 0.99
nstcalclr= -1


Although it use group cut-off scheme, there is also a verlet-buffer-drift, 
which doesn't show in the 2016.3 version .mdp option.

So, lots of thanks for anyone's advice for setting group scheme.

> Given that you are modifying the force field to add different interactions,
> you will anyway have to show that the modified form of the force field
> works suitably. Even if the Verlet scheme had support for tabulated
> interactions, you would still be limited to having only one set of
> nonbonded parameters per atom type. Is your mix of interaction types
> feasible to use with such a restriction?
> 

I'm really looking forward to the combination of Verlet cut-off scheme with the 
tabulated potential. :)

> Mark
> 
> >
> -- 
> 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] Group NS scheme parameter for 2016.3 version

[Du, Yu]

Dear GMX Users, 


Indeed making tabulized potential between groups with Verlet is not trivial as 
also discussed in OpenMM issue #1765. 


I'm using gmx 2016.3. If I want use the group NS scheme as precise as possible, 
what parameters in mdp file should I set and what are their recommended values 
for protein and ligand system.


Thanks for your advice.


Yu
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Re: [gmx-users] Is amber ff compatible with user-specified potential functions?

[Du, Yu]

Dear GMX users, 

Hope you can see this email. 
Thanks for your help.

Yu


> -Original Messages-
> From: "Du, Yu" 
> Sent Time: 2017-09-23 22:58:29 (Saturday)
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc: d...@sioc.ac.cn
> Subject: Re: [gmx-users] Is amber ff compatible with user-specified potential 
> functions?
> 
> Dear GMX users, 
> 
> After several tests, I found that Verlet (2016.3 version) still don't support 
> the vwdtype=user with tabulated potentials:
> 
> ERROR 1 [file md.mdp]:
>   With Verlet lists only cut-off and PME LJ interactions are supported
> 
> So with Verlet on, are there any decent ways to turn off the attractive part 
> of the vwd potential?
> 
> Thanks for your advice. 
> 
> Yu
> 
> 
> > -Original Messages-
> > From: "Du, Yu" 
> > Sent Time: 2017-09-23 19:15:52 (Saturday)
> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> > Cc: 
> > Subject: [gmx-users] Is amber ff compatible with user-specified potential 
> > functions?
> > 
> > 
> > 
> > 
> > 
> > 
> > Dear GMX users, 
> > 
> > 
> > The context of my question is that I want to simulate the interaction 
> > between protein and ligand with Weeks-Chandler-Andersen (WCA), and normal 
> > LJ12-6 potential for others. 
> > mdp file like this
> > energygrps = Protein Ligand, energygrp-table= Protein Ligand
> > So I need the two xvg files: table.xvg, table_Protein_Ligand.xvg.
> > 
> > 
> > Context end 
> > 
> > 
> > 
> > 
> > I'm trying the WCA nbfunc and the main reference is the User Specied 
> > non-bonded potentials in
> > gromacs. This webpage and attached pdf is 7 years old. It said that "If you 
> > specify your own potentials these parameters must be both set equal to 1 
> > (nbfunc and comb-rule)."
> > 
> > 
> > I'm using gromacs 2016.3 version, has this both-to-be-1 condition be 
> > changed and been more flexible?
> > 
> > 
> > And I'm asking that if I use WCA potential and amber ff whose the nbfunc 
> > and comb-rule is 1 and 2, will this conflict with the both-to-be-1 
> > condition? If so, how can I work around this?
> > 
> > 
> > 
> > 
> > Thanks.
> > 
> > 
> > Yu
> > -- 
> > 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] Is amber ff compatible with user-specified potential functions?

[Du, Yu]

Dear GMX users, 

After several tests, I found that Verlet (2016.3 version) still don't support 
the vwdtype=user with tabulated potentials:

ERROR 1 [file md.mdp]:
  With Verlet lists only cut-off and PME LJ interactions are supported

So with Verlet on, are there any decent ways to turn off the attractive part of 
the vwd potential?

Thanks for your advice. 

Yu


> -Original Messages-
> From: "Du, Yu" 
> Sent Time: 2017-09-23 19:15:52 (Saturday)
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Cc: 
> Subject: [gmx-users] Is amber ff compatible with user-specified potential 
> functions?
> 
> 
> 
> 
> 
> 
> Dear GMX users, 
> 
> 
> The context of my question is that I want to simulate the interaction between 
> protein and ligand with Weeks-Chandler-Andersen (WCA), and normal LJ12-6 
> potential for others. 
> mdp file like this
> energygrps = Protein Ligand, energygrp-table= Protein Ligand
> So I need the two xvg files: table.xvg, table_Protein_Ligand.xvg.
> 
> 
> Context end 
> 
> 
> 
> 
> I'm trying the WCA nbfunc and the main reference is the User Specied 
> non-bonded potentials in
> gromacs. This webpage and attached pdf is 7 years old. It said that "If you 
> specify your own potentials these parameters must be both set equal to 1 
> (nbfunc and comb-rule)."
> 
> 
> I'm using gromacs 2016.3 version, has this both-to-be-1 condition be changed 
> and been more flexible?
> 
> 
> And I'm asking that if I use WCA potential and amber ff whose the nbfunc and 
> comb-rule is 1 and 2, will this conflict with the both-to-be-1 condition? If 
> so, how can I work around this?
> 
> 
> 
> 
> Thanks.
> 
> 
> Yu
> -- 
> 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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[gmx-users] Is amber ff compatible with user-specified potential functions?

[Du, Yu]

Dear GMX users, 


The context of my question is that I want to simulate the interaction between 
protein and ligand with Weeks-Chandler-Andersen (WCA), and normal LJ12-6 
potential for others. 
mdp file like this
energygrps = Protein Ligand, energygrp-table= Protein Ligand
So I need the two xvg files: table.xvg, table_Protein_Ligand.xvg.


Context end 




I'm trying the WCA nbfunc and the main reference is the User Specied 
non-bonded potentials in
gromacs. This webpage and attached pdf is 7 years old. It said that "If you 
specify your own potentials these parameters must be both set equal to 1 
(nbfunc and comb-rule)."


I'm using gromacs 2016.3 version, has this both-to-be-1 condition be changed 
and been more flexible?


And I'm asking that if I use WCA potential and amber ff whose the nbfunc and 
comb-rule is 1 and 2, will this conflict with the both-to-be-1 condition? If 
so, how can I work around this?




Thanks.


Yu
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Re: [gmx-users] Concrete pull code explanation needed

[Du, Yu]

> -Original Messages-
> From: "Justin Lemkul" 
> Sent Time: Thursday, July 13, 2017
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Concrete pull code explanation needed
> 
> 
> 
> On 7/11/17 8:23 PM, Du, Yu wrote:
> >> On 7/10/17 11:19 PM, Du, Yu wrote:
> >>> Dear Justin and gmx users,
> >>>
> >>>
> >>> I have gone through mdp-option and Justin A. Lemkul's COM pulling 
> >>> tutorial serveral times.
> >>>
> >>>
> >>> The following is Justin's pull code.
> >>>
> >>>
> >>> ; 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
> >>>
> >>>
> >>> My understanding lists as follows,
> >>>
> >>>
> >>> Justin defines two pull groups, with `pull-ngroups = 2`, each of them has 
> >>> a name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their 
> >>> names are defined by `pull_group1_name = Chain_B` and `pull_group2_name = 
> >>> Chain_A`.
> >>>
> >>>
> >>> My question is about the definition of pulling coordination and the 
> >>> orientation of pulling force.
> >>>
> >>>
> >>> 1) I learnt from [gmx-users] Change to umbrella sampling pull code，
> >>> "You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is 
> >>> undefined, or otherwise defaults to the entire system, I can't remember 
> >>> which. -Justin"
> >>>
> >>>
> >>> I know it's a plot :) in the input.pdb that proteins are placed 
> >>> exquisitely along the z-axis which is the same as the pulling coordinate 
> >>> but it makes pull code confused and here I need a concrete explanation.
> >>> 1.The pull coordinate is the line that connects COM of group1 and group2 
> >>> with `pull_coord1_groups= 1 2`.
> >>> OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
> >>> Which is correct?
> >>>
> >>
> >> The z-component of the vector connecting the COMs of the two groups.
> >>
> >>>
> >>> 2)Then turn to the orientation of pulling forces.
> >>> My understanding is that force1 acts on pull_group1, force2 acts on 
> >>> pull_group2 and the orientation of force 1 and 2 is opposite, both forces 
> >>> have a rate of 10nm per ns.
> >>> Is my understanding and the below schematic draw right?
> >>>
> >>
> >> There is one force.  It acts on the spring connecting the two groups.
> > 
> > 
> > How does the spring connect the two groups? Does the spring link to the COM 
> > of the whole two groups?
> 
> Yes.
> 
> > How does Gromacs define the orientation of the force of pulling? Or by 
> > default is the pulling force just positive along the z axis with 
> > `pull_coord1_geometry = distance` and `pull_coord1_dim = N N Y`?
> > 
> 
> This is not the default, but it is precisely what is specified by those .mdp 
> settings.
> 


Could you please show which line specifies the orientation of the pulling 
force? Is it the positive `pull_coord1_rate`? So `pull_coord1_rate` can be 
either positive or negative?

> >>
> >>>
> >>> Z-axis-0-5--->---positive-orientation--->-25-->
> >>>  <Force1---pull_group1~pull_group2--Force2-->
> >>>
> >>>
> >>> The last question is about the umbrella sampling.
> >>> I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial 
> >>> that it's ok to remove the pores of Chain B during the US. But in longer 
> >>> simulation time and in the periodical box, will the COM of Chain B and A 
> >>> be affacte

Re: [gmx-users] Concrete pull code explanation needed

[Du, Yu]

> On 7/10/17 11:19 PM, Du, Yu wrote:
> > Dear Justin and gmx users,
> > 
> > 
> > I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
> > serveral times.
> > 
> > 
> > The following is Justin's pull code.
> > 
> > 
> > ; 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
> > 
> > 
> > My understanding lists as follows,
> > 
> > 
> > Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
> > name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names 
> > are defined by `pull_group1_name = Chain_B` and `pull_group2_name = 
> > Chain_A`.
> > 
> > 
> > My question is about the definition of pulling coordination and the 
> > orientation of pulling force.
> > 
> > 
> > 1) I learnt from [gmx-users] Change to umbrella sampling pull code，
> > "You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is 
> > undefined, or otherwise defaults to the entire system, I can't remember 
> > which. -Justin"
> > 
> > 
> > I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
> > along the z-axis which is the same as the pulling coordinate but it makes 
> > pull code confused and here I need a concrete explanation.
> > 1.The pull coordinate is the line that connects COM of group1 and group2 
> > with `pull_coord1_groups= 1 2`.
> > OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
> > Which is correct?
> > 
> 
> The z-component of the vector connecting the COMs of the two groups.
> 
> > 
> > 2)Then turn to the orientation of pulling forces.
> > My understanding is that force1 acts on pull_group1, force2 acts on 
> > pull_group2 and the orientation of force 1 and 2 is opposite, both forces 
> > have a rate of 10nm per ns.
> > Is my understanding and the below schematic draw right?
> > 
> 
> There is one force.  It acts on the spring connecting the two groups.


How does the spring connect the two groups? Does the spring link to the COM of 
the whole two groups? 
How does Gromacs define the orientation of the force of pulling? Or by default 
is the pulling force just positive along the z axis with `pull_coord1_geometry 
= distance` and `pull_coord1_dim = N N Y`?

> 
> > 
> > Z-axis-0-5--->---positive-orientation--->-25-->
> > <Force1---pull_group1~pull_group2--Force2-->
> > 
> > 
> > The last question is about the umbrella sampling.
> > I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial 
> > that it's ok to remove the pores of Chain B during the US. But in longer 
> > simulation time and in the periodical box, will the COM of Chain B and A be 
> > affacted by the boundary? and then affact the calculation of US potential?
> > 
> 
> The tutorial system won't work if you turn off the restraint.  Eventually the 
> system will rotate and the groups will cross periodic boundaries, which will 
> cause the chosen pull geometry to fail.  So the restraints serve a dual 
> purpose: 
> (1) to mimic the stability of larger amyloid assemblies and (2) to reduce the 
> system size, as several hundred thousand atoms was not feasible for me at the 
> time.


So your point is that during US, we can't remove the Chain B's restrain. Right?
During US, is there any means to study the flexiblity of both groups? (i.e. 
there is no restrain on both groups except the umbrella potential between them 
and at the same time both groups will not cross periodic boundaries and will 
not affact the umbrella potential geometry, which is a necessary part of my 
study)

Yu


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[gmx-users] Concrete pull code explanation needed

[Du, Yu]

Dear Justin and gmx users, 


I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
serveral times.


The following is Justin's pull code.


; 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


My understanding lists as follows, 


Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names are 
defined by `pull_group1_name = Chain_B` and `pull_group2_name = Chain_A`.


My question is about the definition of pulling coordination and the orientation 
of pulling force.


1) I learnt from [gmx-users] Change to umbrella sampling pull code，
"You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is 
undefined, or otherwise defaults to the entire system, I can't remember which. 
-Justin"


I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
along the z-axis which is the same as the pulling coordinate but it makes pull 
code confused and here I need a concrete explanation.
1.The pull coordinate is the line that connects COM of group1 and group2 with 
`pull_coord1_groups= 1 2`. 
OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`. 
Which is correct? 


2)Then turn to the orientation of pulling forces.
My understanding is that force1 acts on pull_group1, force2 acts on pull_group2 
and the orientation of force 1 and 2 is opposite, both forces have a rate of 
10nm per ns. 
Is my understanding and the below schematic draw right?


Z-axis-0-5--->---positive-orientation--->-25-->
   


The last question is about the umbrella sampling.
I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial that 
it's ok to remove the pores of Chain B during the US. But in longer simulation 
time and in the periodical box, will the COM of Chain B and A be affacted by 
the boundary? and then affact the calculation of US potential?


Best Regards, 
Yu


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Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

[Du, Yu]

Yeah, Thanks for the clue.

> -Original Messages-
> From: "Mark Abraham" 
> Sent Time: Friday, July 7, 2017
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Fatal error: Invalid character in digit-only string: 
> '�'
> 
> Hi,
> 
> Yes. And it looks like you've copied and pasted a "smart quote" character
> produced from some fancy editor. If that's a tutorial or user guide, please
> ask them to fix it ;-)
> 
> Mark
> 
> On Thu, 6 Jul 2017 17:25 Hermann, Johannes 
> wrote:
> 
> > Hey Yu
> >
> > Try:
> >
> > gmx mdrun -v -ntmpi 8 -gpu_id  -deffnm nvt
> >
> > So the same command you used, but _without_ the quotation marks. That is
> > what the error tells you.
> >
> > Best
> > Johannes
> > On 06.07.2017 16:52, Du, Yu wrote:
> > > Dear Gromacs Users,
> > >
> > >
> > > I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5:
> > Protein-Ligand Complex.
> > > If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.
> > >
> > >
> > > If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will
> > get the following errors.
> > >
> > >
> > > Is this a bug or the some error with the installment.
> > > I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this
> > email.
> > > The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4
> > -DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath
> > -Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON
> > -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0
> > -DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3
> > -DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3
> > -DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256
> > -DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so
> > -DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`
> > >
> > >
> > > Thanks for any information about the error, my nvt.log file and the
> > compile command parameters.
> > >
> > >
> > > Yu
> > >
> > >
> > > ===
> > > [duyu@gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “”
> > -deffnm nvt
> > >
> > >
> > > Back Off! I just backed up nvt.log to ./#nvt.log.3#
> > >
> > >
> > > Running on 1 node with total 20 cores, 40 logical cores, 4 compatible
> > GPUs
> > > Hardware detected:
> > >CPU info:
> > >  Vendor: Intel
> > >  Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
> > >  SIMD instructions most likely to fit this hardware: AVX2_256
> > >  SIMD instructions selected at GROMACS compile time: AVX_256
> > >
> > >
> > >Hardware topology: Basic
> > >GPU info:
> > >  Number of GPUs detected: 4
> > >  #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >  #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >  #2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >  #3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
> > >
> > >
> > > Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this
> > machine, which is better.
> > >
> > >
> > > Reading file nvt.tpr, VERSION 2016.3 (single precision)
> > > Changing nstlist from 10 to 40, rlist from 1.4 to 1.472
> > >
> > >
> > >
> > >
> > > ---
> > > Program: gmx mdrun, version 2016.3
> > > Source file: src/gromacs/utility/cstringutil.cpp (line 583)
> > >
> > >
> > > Fatal error:
> > > Invalid character in digit-only string: '�'
> > >
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > > ---
> > > ===
> > > LOG FILE:
> > >
> > > GROMACS version:2016.3
> > > Precision:  single
> > > Memory model:   64 bit
> > > MPI library:thread_mpi
> > >

[gmx-users] Fatal error: Invalid character in digit-only string: '�'

[Du, Yu]

Dear Gromacs Users, 


I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5: Protein-Ligand 
Complex.
If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.


If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will get the 
following errors.


Is this a bug or the some error with the installment.
I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this email. 
The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4 
-DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath 
-Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON 
-DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0 
-DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3 
-DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3 
-DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256 
-DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so 
-DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`


Thanks for any information about the error, my nvt.log file and the compile 
command parameters.


Yu


===
[duyu@gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “” -deffnm 
nvt


Back Off! I just backed up nvt.log to ./#nvt.log.3#


Running on 1 node with total 20 cores, 40 logical cores, 4 compatible GPUs
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX_256


  Hardware topology: Basic
  GPU info:
Number of GPUs detected: 4
#0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
#1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
#2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
#3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible


Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this 
machine, which is better.


Reading file nvt.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1.4 to 1.472




---
Program: gmx mdrun, version 2016.3
Source file: src/gromacs/utility/cstringutil.cpp (line 583)


Fatal error:
Invalid character in digit-only string: '�'


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

GROMACS version:2016.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:CUDA
SIMD instructions:  AVX_256
FFT library:fftw-3.3.6-pl2-sse2-avx
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   Tue Jul  4 17:23:23 CST 2017
Built by:   duyu@gpu-new [CMAKE]
Build OS/arch:  Linux 2.6.32-431.el6.x86_64 x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
Build CPU family:   6   Model: 63   Stepping: 2
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx 
msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 
sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4 GNU 4.9.4
C compiler flags:-mavx   -Wl,-rpath -Wl,/home/duyu/software/gcc-4.9.4/lib64 
 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
C++ compiler:   /home/duyu/software/gcc-4.9.4/bin/g++-4.9.4 GNU 4.9.4
C++ compiler flags:  -mavx-std=c++0x   -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
CUDA compiler:  /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
CUDA compiler 
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;-ccbin=/home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4;;;-Xcompiler;,-mavx,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,;
 
CUDA driver:7.0
CUDA runtime:   7.0
===


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