[gmx-users] Protein potential energy

[Ming Tang]

Dear list,

I pulled a protein in water. In order to get the trend of the potential energy 
terms of the protein, I defined energygrps and reran the system. May I ask can 
I get the right trend of the protein potential energy terms using this approach?

Your help is appreciated.
Thanks,
Tammy

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[gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

[Ming Tang]

Dear list,

I have gone through carbon nanotube guide on GROMACS website.
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
I have a nanotube aligned to z-direction. I am trying to simulate infinite 
nanotube using periodic conditions. There are issues while simulating this 
system when pressure coupling is used.

GROMACS or other mailing list doesn't provide mdp files for simulation of 
carbon nanotube using NPT ensemble. It appears that we cannot freeze groups to 
constrain nanotube in NPT ensemble. We might have to use position restraints 
for nanotube (most papers report this). I have imposed position restraints on 
nanotube and in doing so, the z coordinates fluctuates by 0.5-1 nm in Z 
direction. This is not an issue with NVT simulation.

How do I equilibrate nanotube system using pressure coupling for 
nonotube/graphene etc with infinite long surface? Should we use semi-isotropic 
scheme (not apply pressure along the axis of nanotube) for pressure coupling or 
it should be isotropic?

P.S.: the force field is opls based on gromacs tutorial and GROMACS version is 
5.1.4. Temperature coupling -V-rescale

Thanks,
Ming on behalf of Neha
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Re: [gmx-users] How to convert C6 from GROMOS54a7 to sigma for OPLSAA

[Ming Tang]

Hi Justin, thanks for your guidance!

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[gmx-users] How to convert C6 from GROMOS54a7 to sigma for OPLSAA

[Ming Tang]

Dear all,

I want to calculate sigma for OPLSAA.ff from C6 developed based on 
GROMOS54a7.ff.

>From the manual, I got the equations:



C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon
However, I found sigma and epsilon are different in OPLSAA and AMBER, and that 
C6 from GROMOS and sigma from OPLSAA do not match these equations. 
Could anybody give me some guidance?

Thanks,
Ming
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[gmx-users] g_energy error

[Ming Tang]

Dear list,

I want to investigate the trend of the potential energy of the protein in my 
system with water.
I run :
trjconv -f md.trr -o protein.xtc
tpbconv -s topol.tpr -o protein.tpr
mdrun -rerun protein.xtc -s protein.tpr

I got the following errors:

WARNING: there may be something wrong with energy file ener.edr
Found: step=-1, nre=38, nblock=0, time=1.0185e+06.
Trying to skip frame expect a crash though

Then I obtained ener.edr file , and run :
g_energy -f ener.edr -o potential.xvg

I got the same erros.
However, the trend of the obtained potential looks reasonable.

Could anybody give me some suggestions about this?

Thank you,
Tammy

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Re: [gmx-users] pulling with constant force

[Ming Tang]

Hi list,


I fixed it by setting 'pull-coord1-vec = -1 0 0'
Thanks.
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[gmx-users] pulling with constant force

[Ming Tang]

Dear list,

I want to pull my protein away from each other using a constant force. I fix 
one end (group 'start') and used the following pull code but found that 2 
pulling groups are getting closer no matter whether I set pull-coord1-k  as 
1000 or -1000.


; COM pulling.
pull= constant-force
pull-geometry   = direction-periodic
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= start
pull-group2-name= end
pull-coord1-k   = 1000
pull-coord1-vec = 1 0 0

is my code correct? Do I have to set a virtual point to pull the 'end' group?

Your help will be appreciated!
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[gmx-users] convert amber topology and coordinates files into gromacs topology

[Ming Tang]

Dear list,

I am studying glycoprotein. As amber is very slow on CPUs, I really want to do 
my simulations in gromacs. I found that gromacs has amber99sb.ff. So I want to 
convert amber topology and coordinates files into gromacs topology using 
Antechamber. My concerns are:

1)  amber16 has leaprc.protein.ff14SB now, then is it reliable to study my 
glycoprotein using amber99sb.ff in gromacs?

2)  If amber99sb.ff in gromacs is reliable, will the topology changing 
process using Antechamber affect the simulation results?

Thank you,
Tammy
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Re: [gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

[Ming Tang]

Thanks Justin,

mdrun -rerun works. But I failed to fix it via gmx traj with this command:
gmx traj -f traj_comp.xtc -s topol.tpr -ox pullfx.xvg -of pullf.xvg -dt 400

error say .xtc file do not have force information.
Is the command I used correct?
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[gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

[Ming Tang]

Dear list,

I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared 
to the traj_comp.xtc. is it possible to get a more frequently written pull COM 
coordinates and forces based on the traj_compxtc file I have?

Thank you,
Ming
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[gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

[Ming Tang]

Dear list,

I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared 
to the traj_comp.xtc. is it possible to get a more frequently written pull COM 
coordinates and forces based on the traj_compxtc file I have?

Thank you

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Re: [gmx-users] how to distance between COM of two groups of atoms?

[Ming Tang]

Fixed!
Thanks.
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Re: [gmx-users] how to distance between COM of two groups of atoms?

[Ming Tang]

Thank you Justin,

I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon 
atoms. I used the following command to calculate the distance between COM of 
those 2 groups

gmx distance -n index.ndx -select 'com of group "start" plus com of group 
"end"' -f test.pdb -s topol.tpr -oxyz dist.xvg

and got average distance:4.385, which is not correct as my protein is around 
30-nm-long.

is the command I used correct?
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[gmx-users] how to distance between COM of two groups of atoms?

[Ming Tang]

Dear list,

I found that gmx distance can calculate distance between 2 atoms. is there a 
way to calculate distance centre of mass between 2 group of atoms?

Thanks,
Ming
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[gmx-users] hbond between backbone atoms

[Ming Tang]

Dear list,

I want to calculate hbond between backbone atoms on different chains of my 
protein only. but when it give me this error "nothing to be none".
I used this command: gxm hbond -f traj.trr  -s topol.tpr -num hbnum.xvg -a 30  
-r 0.5
I can use this command to get hbond between protein and protein.
Can anybody give me some suggestions?

Thank you
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[gmx-users] how to order gpus on different nodes

[Ming Tang]

Dear experts,

I can order 2 gpus on one node from HPC using the following script:

#PBS -l select=1:ncpus=2:ngpus=2:mpiprocs=2:mem=2gb

mpiexec_mpt -n 2 gmx_mpi mdrun -v -deffnm npt -nb gpu -gpu_id 01 -ntomp 2

however when I used the following script to order 4 gpus on 2 nodes, it gave me 
an error saying gpu cannot be detected.

#PBS -l select=2:ncpus=2:ngpus=2:mpiprocs=2:mem=4gb


mpiexec_mpt -n 4 gmx_mpi mdrun -cpi -cpo -c relax.pdb -nb gpu -gpu_id 0011 
-ntomp4

Does anybody know how to order gpus on different nodes?

Thank you.


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[gmx-users] GPUs performance on Gromacs calculation

[Ming Tang]

Dear experts,

I did SMD on 2 M2090 GPUs and 16 CPUs on one node. The simulation ran around 
500 steps every 15 minutes.
However, the SMD simulation ran around 68000 steps using 96 CPUs without GPU.
Is this because the M2090 GPU type works badly on Gromacs?

Our Uni has the following types of GPU. Could anybody help to tell me which one 
is better for my SMD simulation?

* 4 x M2050 Nvidia Tesla GPUs
* 8 x M2090 Nvidia Tesla GPUs (2 per node)
* 12 x K40 Nvidia Tesla GPUs (2 per node)
* 8 x Intel Xeon Phi 5110P Co-processors (2 per node)
* 1 x Bitware S5-PCIe-HQ with Altera Stratix V FPGA

Thank you.
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Re: [gmx-users] bond_atomtype

[Ming Tang]

Thank you Justin, SI in ffnonbonded.itp is correct.
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[gmx-users] bond_atomtype

[Ming Tang]

Dear list,


I want to add parameters for silicon in oplsaa.ff


In .rtp I added:


[ SI ]
 [ atoms ]
SI   opls_966   4.000 0

In .atp I added:


 opls_966   28.08000  ; Si


In ffnonbonded.itp I added:


opls_966   Si4+   1428.08000 4.000   A4.43500e-01  3.98000e-01


In ions.itp I added:


[ moleculetype ]
; molname   nrexcl
SI  1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   opls_9661   SI  SI   1  4   28.0800


when I run this comman:

grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
I got this error:
Unknown bond_atomtype SI

Did I miss something or modify wrongly?

Thank you,
Ming

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Re: [gmx-users] pdb2gmx generate .itp file for each molecule

[Ming Tang]

Hi ,

Maybe you can try -merge all when using pdb2gmx.
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Re: [gmx-users] confusion on energy for a system of protein sovated in water

[Ming Tang]

Thanks Justin,

How about LJ and Coulomb  energy?

I want to see the trend of protein energy only. I defined 2 energy group: 
protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein 
option when using g_energy. Are they VDW and Coulomb force within the protein 
only?


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[gmx-users] confusion on energy for a system of protein sovated in water

[Ming Tang]

Dear lists,

After pulling a protein in water and performing mdrun -rerun, I found that 
G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original 
system using g_energy -f ener.edr , and from the -rerun system using g_energy 
-f rerun.edr have different values.  Firstly, are those values the energy of 
the system? Secondly, why are they different?

Thanks,
Ming
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Re: [gmx-users] fix COM

[Ming Tang]

Hi Mark,

When I submitted my job to our HPC sever, I got this error message:
gromacs/5.0.4(14):ERROR:151: Module 'gromacs/5.0.4' depends on one of the 
module(s) ''
gromacs/5.0.4(14):ERROR:102: Tcl command execution failed: prereq mpt/2.10

I have been told that the mpt version has been updated to 2.13.  So, I am 
wondering whether my gromacs 5.0.4 version is not new enough, as when the mpt 
version on hpc is 2.10, gromacs 5.0.4 works.

Thanks,
Ming
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Re: [gmx-users] fix COM

[Ming Tang]

Thank you Mark,

Could you please help to give more instructions on how to generate restraints 
on a centre of mass virtual site? I know genrestr can implement restraints, but 
I have no idea how to set a virtual site.

BTW:  is the latest version suitable for mpt 2.13?  it seems that version 5.0.4 
does not work.

Thanks,
Ming
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Re: [gmx-users] fix COM

[Ming Tang]

Hi Justin,

Thanks for your information. My atom group contains only 3 atoms, each of which 
is on one chain of a triple helix. Flat-bottomed is new for me. I went through 
section 4.3.2 in the manual, but still feel confused about how to get the 
parameters and how to apply constraints. Do you think flat-bottomed is suitable 
for my case?

Thank you,
Ming
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[gmx-users] fix COM

[Ming Tang]

Dear Gromacs experts,

Is there a approach to fix the centre of mass of a group of atoms only without 
fixing all of the atoms during a stretching process?

Regards,
Ming
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[gmx-users] the helical axis of a triple helix

[Ming Tang]

Dear list,

I want to calculate the trajectory of the helical axis of a triple helix. Do 
you have any suggestions for me to achieve this?
Any suggestions is appreciated.

Thanks,
Ming

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Re: [gmx-users] Weird configuration when pulling rate is small

[Ming Tang]

Dear Erik,

Thanks for your advice. I think you are right. However, when using -pbc whole, 
every chain is intact but the three chains separate in some frames; when using 
-pbc nojump, the collagen molecule is not intact (there is a small part stay in 
the other box ) either. If I fix one end, and use -pbc whole, the problem is 
fixed.
Thanks and regards,
Ming
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[gmx-users] Weird configuration when pulling rate is small

[Ming Tang]

Dear list,

I am pulling a triple helix using umbrella distance. When the pulling rate is 
0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling 
rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow away 
from the triple helix), but the simulations run well and both the force_strain 
curve and the history of number of h_bonds  look normal. Could anybody tell me 
why is that low pulling rates cause this problem?

Thanks in advance,
Ming

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Re: [gmx-users] weird configuration when pulling rate is small

[Ming Tang]

Hi Tsjerk,

I tried, and got the same configuration.  Initially, I add -nojump when using 
g_traj.
I am not sure whether it has something to do with the pulling method (umbrella 
distance). In reference, researchers use SMD (fix the COM of one group, and 
stretch the COM of the other group). But I did not find a solution to achieve. 
So I stretched the COM of both ends using umbrella distance.

Thanks,
Ming
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[gmx-users] weird configuration when pulling rate is small

[Ming Tang]

Dear list,

I am pulling a triple helix using umbrella distance. When the pulling rate is 
0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling 
rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow far 
away), but the simulations run well and the force_strain curve is normal. Could 
anybody help to tell me where is the problem?

Thanks in advance,
Ming
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[gmx-users] difference between entropic energy and free energy

[Ming Tang]

Deer list,

I am quite confused about the concept of entropic energy and free energy. Could 
anybody help to tell me what is the difference between them?

Thanks.
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Re: [gmx-users] A question about simulation system includes more than 100000 atoms using Gromacs

[Ming Tang]

my system includes1,700,000 atoms, and runs well with 5.0.4.

Sent from my Huawei Mobile

张竹青 zhuqingzh...@ucas.ac.cn wrote:

Dear Madam/Sir,

  I have recently tried to use Gromacs to simulation a biolmoleculal system 
including more than 10 atoms. As usually, the .gro file just supports the 
system with atom number up to 9. But there are some publications in which 
researchers used Gromacs to simulate like ribosom systems, which includes more 
than 200 atoms. So, could you give some advice on how to do it? Does it 
need to change the source codes?

  Thanks,

  Zhuqing










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Re: [gmx-users] LJ-14 energy

[Ming Tang]

Dear Justin,

Thanks very much for your explanation, my confusion on LJ energy has gone now. 
Besides, thank you for telling me my assuming is incorrect.

Regards.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 16 July 2015 9:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LJ-14 energy



On 7/16/15 7:08 AM, Ming Tang wrote:
 Dear Justin,

 Thanks. 1.  The total Lennar-Jones 12-6 energy of the whole system is 
 the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb 
 energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my 
 understanding of your explanation right? Besides, in Gromacs, is the 
 potential energy the addition of G96Bond, G96Angle, Proper-Dih, 
 Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR and 
 Coulomb-LR? You are right. That's why I don't

Well, that's the exact definition of an additive functional form, so yes.

 get the LJ-LR and Coulomb-LR options when using g_energy. Suddenly, I 
 realised that my understanding of the twin-range approach was totally wrong.
 For cutoff-scheme = verlet, rlist cannot be smaller than rvdw = 
 rcoulomb, and When using twin-range method, either coulombtype = 
 cut-off with rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. 
 Does this mean that for twin-range approach, rlist = rcoulomb = rvdw when 
 cutoff-scheme =  verlet?
 However, even if I set vdw-modifier = potential- switch, the rlistlong 
 larger than rlist is reset to be equal to rlist by gromacs, and there 
 is not LJ-SR option when using g_energy. I am totally lost. Can you 
 help to tell me how does twin-range work when cutoff-scheme = verlet? 
 Another question is I used the following code to make my cut-off 
 parameters be consistent with those used for the triple-range cut-off 
 scheme in the paper defining Gromos 54a7 force field:

 coulombtype  =  reaction-field coulomb-modifier =  potential-shift
 rcoulomb-switch  =  0.8 rcoulomb =  1.4 epsilon_rf   =  61

 Currently, I think it is wrong. It seems that rlist = 0.8 is 
 reasonable. But rlist should not be smaller than rcoulomb when 
 cutoff-scheme = verlet. How to achieve this triple-range cut-off scheme?


I honestly have no idea.  I don't use GROMOS force fields any more.  With the 
group scheme, it is easy, but with Verlet I have no idea what the equivalent 
approach is.

 2.   The pull rate I use is 4e-5/ps. I thought it is small so that the energy
 of water can be treated as constant during the pull process. I forgot 
 to consider the water-protein interaction and that my pull rate is 
 much larger than the pull rates used in the experiments which is in 
 order of micrometre per second and is much more relevant to 
 physiological pulling rate. You are right, I cannot treat the trends 
 of the system's energy as those of the protein's energy. But how can I 
 get the energy of the protein? Is it feasible to set all the atoms of 
 the protein as one energy group, and do rerun to achieve this?


The energy of the protein is not a useful quantity.  It is a force 
field-specific quantity.  Energy differences and free energies are valuable.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] LJ-14 energy

[Ming Tang]

Dear Justin,

Thanks.
1.  The total Lennar-Jones 12-6 energy of the whole system is the addition of 
LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of 
coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation 
right? Besides, in Gromacs, is the potential energy the addition of G96Bond, 
G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR 
and Coulomb-LR?
You are right. That's why I don't get the LJ-LR and Coulomb-LR options when 
using g_energy. Suddenly, I realised that my understanding of the twin-range 
approach was totally wrong. For cutoff-scheme = verlet, rlist cannot be smaller 
than rvdw = rcoulomb, and When using twin-range method, either coulombtype = 
cut-off with 
rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean that 
for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme =  verlet? 
However, even if I set vdw-modifier = potential- switch, the rlistlong larger 
than rlist is reset to be equal to rlist by gromacs, and there is not LJ-SR 
option when using g_energy. I am totally lost. Can you help to tell me how does 
twin-range work when cutoff-scheme = verlet?
Another question is I used the following code to make my cut-off parameters be 
consistent with those used for the triple-range cut-off scheme in the paper 
defining Gromos 54a7 force field:

coulombtype  =  reaction-field
coulomb-modifier =  potential-shift
rcoulomb-switch  =  0.8
rcoulomb =  1.4
epsilon_rf   =  61

Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable. But 
rlist should not be smaller than rcoulomb when cutoff-scheme = verlet. How to 
achieve this triple-range cut-off scheme?

2.   The pull rate I use is 4e-5/ps. I thought it is small so that the energy 
of water can be treated as constant during the pull process. I forgot to 
consider the water-protein interaction and that my pull rate is much larger 
than the pull rates used in the experiments which is in order of micrometre per 
second and is much more relevant to physiological pulling rate. You are right, 
I cannot treat the trends of the system's energy as those of the protein's 
energy. But how can I get the energy of the protein? Is it feasible to set all 
the atoms of the protein as one energy group, and do rerun to achieve this?

Thanks,
Regards 
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 16 July 2015 11:20 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LJ-14 energy



On 7/15/15 8:39 PM, Ming Tang wrote:
 Dear Chaban and Justin,



 Sorry for the mis-action. Please ignore my last email.



 Thank you both for your free help.

 I am pulling a collagen triple helix in a periodic water box using 
 umbrella direction-periodic. I want to calculate the Lennard-Jones 
 12-6 of the protein. According to Gromacs manual, it contains 
 repulsive short-range term and attractive long-range term. Is the 
 Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am 
 interested in the energy trends more than

LJ-LR only exists with a twin-range cutoff approach.  The total LJ between any 
groups also includes LJ-14 for intramolecular terms.  Intermolecular LJ would 
be the sum of LJ-SR and LJ-LR, if the latter exists.

 the energy absolute values. So, if I can calculate the LJ 12-6 of the 
 whole system, it is fine, because I can assume the energy of the water 
 is not subject to change due to pulling.


Why can you assume that?  You're pulling a structure, which is a 
non-equilibrium process.  There will be different interactions as a function of 
time. 
Water-water interactions at long distance from the protein indeed are unlikely 
to be affected, but those close to the protein may be different (though 
electrostatics/hydrogen bonding are probably much more interesting). 
Water-protein interactions certainly can't be assumed to be unchanging during 
pulling.

-Justin

--
==

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

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

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

==
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[gmx-users] LJ-14 energy

[Ming Tang]

Dear Gromacs experts,

I am confused about the meaning of LJ-14 option in g_energy. I checked the 
achieve, and found that Justin said it stands for intramolecular interactions 
between atoms separated by 3 bonds. My simulation is protein solvated in water. 
How can I calculate the Lennard-Jones potential energy of the whole system?
I found that if I set 2 energy groups and rerun, there will be options like 
LJ-14: protein-ions. So, how does Gromacs calculate those energy?

Another problem I came across is the LJ-14 I got is weird.  The Coulomb-14 
energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to -700 
and then increase to- 400, followed by a linear decline to -1700. The LJ-14 
should increase, am I right?

Here is part of my .mdp

cutoff-scheme=  verlet
ns_type  =  grid
coulombtype  =  reaction-field
coulomb-modifier =  potential-shift
rcoulomb-switch  =  0.8
rcoulomb =  1.4
epsilon_rf   =  61
vdwtype  =  cut-off
vdw-modifier =  force-switch
rvdw-switch  =  0.8
rvdw =  1.4

To find out the reason, I checked the manual. It says for vdwtype = switch or 
vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than rvdw. 
As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for the 
simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is this the 
reason of the weird LJ-14?
Another question is, is vdw-modifier = force switch more accurate than 
vdw-modifier = potential - shift?

Any help will be appreciated.

Regards
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Re: [gmx-users] [gm.-users] LJ-14 energy

[Ming Tang]

Dear Chaban and Justin,

Thank you both for your free help.
I am pulling a collagen triple helix in a periodic water box using umbrella 
direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. 
According to Gromacs manual, it contains repulsive short-range term and 
attractive long-range term. Is the Lennard-Jones 12-6 energy 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Wednesday, 15 July 2015 11:36 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LJ-14 energy



On 7/15/15 5:27 AM, Ming Tang wrote:
 Dear Gromacs experts,

 I am confused about the meaning of LJ-14 option in g_energy. I checked the 
 achieve, and found that Justin said it stands for intramolecular interactions 
 between atoms separated by 3 bonds. My simulation is protein solvated in 
 water. How can I calculate the Lennard-Jones potential energy of the whole 
 system?
 I found that if I set 2 energy groups and rerun, there will be options like 
 LJ-14: protein-ions. So, how does Gromacs calculate those energy?


Intermolecular LJ-14 are by definition zero and actually do not correspond to 
anything real, anyway.  Just a quirk of the decomposition of nonbonded terms in 
the code.

-Justin

This does make sense! Your explanation is always clear and precious. I found 
that LJ-14: protein-ions of my system is really zero.

 Another problem I came across is the LJ-14 I got is weird.  The Coulomb-14 
 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to 
 -700 and then increase to- 400, followed by a linear decline to -1700. The 
 LJ-14 should increase, am I right?


Depends on what's happening.  There's no reason to think that any energy term 
will inherently show any trend, but the outcome reflects whatever is happening 
in the dynamics.

 Here is part of my .mdp

 cutoff-scheme=  verlet
 ns_type  =  grid
 coulombtype  =  reaction-field
 coulomb-modifier =  potential-shift
 rcoulomb-switch  =  0.8
 rcoulomb =  1.4
 epsilon_rf   =  61
 vdwtype  =  cut-off
 vdw-modifier =  force-switch
 rvdw-switch  =  0.8
 rvdw =  1.4

 To find out the reason, I checked the manual. It says for vdwtype = switch or 
 vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than 
 rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for 
 the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is 
 this the reason of the weird LJ-14?

I think you're mis-reading the manual.  If you set verlet-buffer-tolerance = 
-1, whatever value of rlist you specify (which you haven't shown, so it 
defaults to
1) is used.  You say you did *not* set verlet-buffer-tolerance explicitly, so 
it defaults to a value of 0.005 and rlist is tuned as needed.  The .log file 
will have information as to what rlist was used.

-Justin

I did not set value for verlet-buffer-tolerance and rlist. It turns out that I 
made a silly mistake. I checked the mdout.mdp rather than the mg.log file for 
rlist value. According to mg.log file, Gromacs set rlist = 1.47, which is just 
0.7 larger than rvdw = 1.4. Is this possible to cause any accuracy problems for 
LJ energy?

 Another question is, is vdw-modifier = force switch more accurate than 
 vdw-modifier = potential - shift?


The method used depends on what the force field needs.

-Justin

I use GROMOS 54a7 force field. In the paper defining this ff, I only found the 
method and parameters used to calculate coulomb force, but did not see those 
for van der waals force.  Therefore, I randomly chose vdwtype = cut-off and 
vdw-modifier = force switch. Can you give me some guidance about which method 
and parameters used to calculate the vdw interaction are more suitable for 
GROMOS 54a7 ff?

--
==

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

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

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

==
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[gmx-users] LJ-14 energy

[Ming Tang]

Dear Chaban and Justin,



Sorry for the mis-action. Please ignore my last email.



Thank you both for your free help.

I am pulling a collagen triple helix in a periodic water box using umbrella 
direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. 
According to Gromacs manual, it contains repulsive short-range term and 
attractive long-range term. Is the Lennard-Jones 12-6 energy simply the 
addition of LJ-SR and LJ-LR? I am interested in the energy trends more than the 
energy absolute values. So, if I can calculate the LJ 12-6 of the whole system, 
it is fine, because I can assume the energy of the water is not subject to 
change due to pulling.



Thanks.



-Original Message-

From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.semailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul

Sent: Wednesday, 15 July 2015 11:36 PM

To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org

Subject: Re: [gmx-users] LJ-14 energy







On 7/15/15 5:27 AM, Ming Tang wrote:

 Dear Gromacs experts,



 I am confused about the meaning of LJ-14 option in g_energy. I checked the 
 achieve, and found that Justin said it stands for intramolecular interactions 
 between atoms separated by 3 bonds. My simulation is protein solvated in 
 water. How can I calculate the Lennard-Jones potential energy of the whole 
 system?

 I found that if I set 2 energy groups and rerun, there will be options like 
 LJ-14: protein-ions. So, how does Gromacs calculate those energy?





Intermolecular LJ-14 are by definition zero and actually do not correspond to 
anything real, anyway.  Just a quirk of the decomposition of nonbonded terms in 
the code.



-Justin



This does make sense! Your explanation is always clear and precious. I found 
that LJ-14: protein-ions of my system is really zero.



 Another problem I came across is the LJ-14 I got is weird.  The Coulomb-14 
 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to 
 -700 and then increase to- 400, followed by a linear decline to -1700. The 
 LJ-14 should increase, am I right?





Depends on what's happening.  There's no reason to think that any energy term 
will inherently show any trend, but the outcome reflects whatever is happening 
in the dynamics.



 Here is part of my .mdp



 cutoff-scheme=  verlet

 ns_type  =  grid

 coulombtype  =  reaction-field

 coulomb-modifier =  potential-shift

 rcoulomb-switch  =  0.8

 rcoulomb =  1.4

 epsilon_rf   =  61

 vdwtype  =  cut-off

 vdw-modifier =  force-switch

 rvdw-switch  =  0.8

 rvdw =  1.4



 To find out the reason, I checked the manual. It says for vdwtype = switch or 
 vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than 
 rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for 
 the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is 
 this the reason of the weird LJ-14?



I think you're mis-reading the manual.  If you set verlet-buffer-tolerance = 
-1, whatever value of rlist you specify (which you haven't shown, so it 
defaults to

1) is used.  You say you did *not* set verlet-buffer-tolerance explicitly, so 
it defaults to a value of 0.005 and rlist is tuned as needed.  The .log file 
will have information as to what rlist was used.



-Justin



I did not set value for verlet-buffer-tolerance and rlist. It turns out that I 
made a silly mistake. I checked the mdout.mdp rather than the mg.log file for 
rlist value. According to mg.log file, Gromacs set rlist = 1.47, which is just 
0.7 larger than rvdw = 1.4. Is this possible to cause any accuracy problems for 
LJ energy?



 Another question is, is vdw-modifier = force switch more accurate than 
 vdw-modifier = potential - shift?





The method used depends on what the force field needs.



-Justin



I use GROMOS 54a7 force field. In the paper defining this ff, I only found the 
method and parameters used to calculate coulomb force, but did not see those 
for van der waals force.  Therefore, I randomly chose vdwtype = cut-off and 
vdw-modifier = force switch. Can you give me some guidance about which method 
and parameters used to calculate the vdw interaction are more suitable for 
GROMOS 54a7 ff?



--

==



Justin A. Lemkul, Ph.D.

Ruth L. Kirschstein NRSA Postdoctoral Fellow



Department of Pharmaceutical Sciences

School of Pharmacy

Health Sciences Facility II, Room 629

University of Maryland, Baltimore

20 Penn St.

Baltimore, MD 21201



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



==

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Re: [gmx-users] difference between steep and cg

[Ming Tang]

Hi Tsjerk,

This link really helps.

Thank you.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Saturday, 11 July 2015 5:46 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] difference between steep and cg

Hi Ming Tang,

See https://en.m.wikipedia.org/wiki/Gradient_descent
It has a further link to CG.

Cheers,

Tsjerk
On Jul 11, 2015 4:10 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear Gromacs experts,

 I am quite confused about the difference between the energy 
 minimization algorithm steep and cg. According to my experience, MPI 
 is not suitable for cg. Sometimes, even if the system has already 
 converged using steep algorithm, it can be further minimized if one changes 
 the algorithm to cg.
 However, most of the publications choose to use steep descent algorithm.
 Which one is more accurate? Is cg only suitable for specific analysis 
 like normal mode analysis?

 Thanks in advance,

 --
 Gromacs Users mailing list

 * Please search the archive at
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Re: [gmx-users] restrain COM of a group of atoms

[Ming Tang]

Dear Chaban,

Thanks for your explanation, and sorry for the late reply. I didn't notice the 
error when doing mdrun. For one pull-coordn-groups, we need to define two 
groups. So my aforementioned code is not correct.  But I still did not find out 
a way feasible to restrain the COM of the reference group. Can you give me some 
further suggestions?

Thanks a lot.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
V.V.Chaban
Sent: Sunday, 5 July 2015 10:46 PM
To: gmx-users
Subject: Re: [gmx-users] restrain COM of a group of atoms

I do now know what authors meant. However, the COM-COM pulling implies that one 
group is restrained and another group moves relative to it.
So, the COM of the reference group is already fixed in the pull code.



On Sun, Jul 5, 2015 at 4:02 AM, Ming Tang qut20181...@gmail.com wrote:
 Dear Gromacs experts and users,

 I am here to seek help. I want to use constraint pull method to pull a 
 filament. My plan is to keep the center of mass of one group fixed
 through a stiff restraint, say 3×10e5, and pull the other group. I 
 tried to generate the restraint .itp file and modify the topol ifle, 
 but found that I can only restrain all of the atoms, not the COM of 
 the group. There are 2 journals, in which the authors said they used this 
 method like this:
 To apply uniaxial tension, the center of mass of the N-terminal C − α 
 atoms of the two chains was fixed by a stiff harmonic spring and 
 referred as the reference group. they used GROMACS 4.6. I am using 
 version 5.0.4. I tried to use pull code to achieve this, but failed. My code 
 is like this:

 pull= constraint
 pull-geometry   = direction-periodic
 pull-start  = yes
 pull-ngroups= 2
 pull-ncoords= 2
 pull-coord1-groups  = 1
 pull-coord2-groups  = 2
 pull-group1-name= G1
 pull-group2-name= G2
 pull-coord1-rate= 0.0005
 pull-coord2-rate= 0
 pull-coord1-k   = 4000
 pull-coord2-k   = 30
 pull-coord1-vec = 1 0 0
 pull-coord2-vec = 1 0 0

 using this pull code, I found that only the displacement along Z 
 direction of  COM of  G1 was 0 during the simulation, and the 
 displacement along both x direction and y direction changed.

 Could anybody give me some guidance?

 Thanks.
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[gmx-users] difference between steep and cg

[Ming Tang]

Dear Gromacs experts,

I am quite confused about the difference between the energy minimization 
algorithm steep and cg. According to my experience, MPI is not suitable for cg. 
Sometimes, even if the system has already converged using steep algorithm, it 
can be further minimized if one changes the algorithm to cg. However, most of 
the publications choose to use steep descent algorithm. Which one is more 
accurate? Is cg only suitable for specific analysis like normal mode analysis?

Thanks in advance,

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[gmx-users] restrain COM of a group of atoms

[Ming Tang]

Dear Gromacs experts and users,

I am here to seek help. I want to use constraint pull method to pull a
filament. My plan is to keep the center of mass of one group fixed
through a stiff restraint, say 3×10e5, and pull the other group. I tried to
generate the restraint .itp file and modify the topol ifle, but found that
I can only restrain all of the atoms, not the COM of the group. There are 2
journals, in which the authors said they used this method like this:
To apply uniaxial tension, the center of mass of the N-terminal C − α atoms
of the two chains was fixed by a stiff harmonic spring and referred as the
reference group. they used GROMACS 4.6. I am using version 5.0.4. I tried
to use pull code to achieve this, but failed. My code is like this:

pull= constraint
pull-geometry   = direction-periodic
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 2
pull-coord1-groups  = 1
pull-coord2-groups  = 2
pull-group1-name= G1
pull-group2-name= G2
pull-coord1-rate= 0.0005
pull-coord2-rate= 0
pull-coord1-k   = 4000
pull-coord2-k   = 30
pull-coord1-vec = 1 0 0
pull-coord2-vec = 1 0 0

using this pull code, I found that only the displacement along Z direction
of  COM of  G1 was 0 during the simulation, and the displacement along both
x direction and y direction changed.

Could anybody give me some guidance?

Thanks.
-- 
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[gmx-users] how to define wall-atomtype?

[Ming Tang]

Dear all,

I want to pull a collagen in NPT using direction-periodic, and have to use 
pbc=xy with wall. I checked both manual and .mdp options and searched mailing 
lists regarding wall definition in google, but am still have no idea how to 
define wall-atomtype. I want to use 12-6 wall type. Could anybody give me some 
suggestions?

Thanks in advance.

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Re: [gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear Justin,

I tried to equilibrate my collagen with all the heavy atoms restrained using 
define = -DPOSRES in NPT for 300 ps, but found that the collagen became much 
shorter. The restrained force for the heavy atoms generated through pdb2gmx is 
1000 kJ/mol/nm by default, why does the length changed a lot?

Thank you.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 18 June 2015 9:34 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation



On 6/18/15 6:28 AM, Ming Tang wrote:
 Dear Tsjerk and Justin,

 Thanks for your help. I have tried to use 1000 and 1 to restrained the 
 whole protein during NPT equilibration, but found the protein shape changed 
 as well. Is position restraint compatible with pressure coupling?


Restraints are compatible with pressure coupling.  Too high of a restraint can 
generate spurious forces, as Tsjerk mentioned below.  Note that restraints are 
just biasing potentials; they can allow for small changes in the structure.  
You shouldn't necessarily hike the force constant to some high value to try to 
absolutely fix the atoms.

-Justin

 Thanks very much.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Tsjerk Wassenaar
 Sent: Wednesday, 17 June 2015 1:53 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] confusion on NPT MD simulation

 Hi Ming Tang,

 You don't need a huge force constant to keep it fixed. Too high forces may 
 give instabilities. And a more gentle one (100-1000) does the trick as well.

 Cheers,

 Tsjerk
 On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear Justin,

 Thank you so much.  There are another 2 papers in which the authors 
 said they equilibrated their  collagen like this. This really made me 
 confused for quite a  long time, and I come to you for help finally.
 Critical analysis is important.

 In the steps to perform a simulation page, step 8  indicates that 
 NPT equilibration is for fixing the density. I have been confused 
 about how should I equilibrate my collagen before SMD simulation. I 
 want to keep the shape (do not change its length) of my collagen 
 during equilibration, so that the force-deformation curve will not be 
 changed because of the equilibration process. After knowing that 
 freezing and pressure coupling is incompatible, I tried to use NVT 
 with heavy atoms restrained by using -DPOSRES, and further the 
 simulation to SMD (actually umbrella and direction-periodic are used) 
 directly in NVT. The simulation run smoothly and I got my 
 force-deformation curve, but I am still concerned whether my 
 equilibration is good enough for SMD simulation, and whether the results are 
 credible.
 If I choose to further equilibrate my collagen in NPT after in NVT, 
 is it feasible to restrain parts (backbone, terminal atoms) of my 
 collagen by adding a huge force constant (say 1*10e6  kJ/mol/nm^2) 
 through -fc in genrestr command, so that its shape will be reserved 
 during the equilibration?

 Could you please kindly give me some guidance on which is the best 
 equilibration process I show follow to get a good starting point for 
 SMD
 (umbrella+direction-periodic) simulation?

 Thank you so much.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
 Justin Lemkul
 Sent: Tuesday, 16 June 2015 9:37 PM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] confusion on NPT MD simulation



 On 6/16/15 5:27 AM, Ming Tang wrote:
 Dear Justin,

 I read a paper, in which the author equilibrated the collagen like this:
 Firstly, a 100 ps NVT MD simulation at a temperature 310 K was 
 performed, in which velocity rescaling algorithm with 1ps coupling 
 constant was used. Rigid bonds were used to constraint covalent bond 
 length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble 
 with 1bar pressure was used to equilibrate the system while keeping 
 the temperature at 310 K, where Berendsen barostat with 1ps coupling 
 constant was adopted. In this step, the whole protein was held fixed.
 Lastly, we further equilibrated the system in a NPT ensemble for 
 400ps, with a more accurate pressure coupling algorithm based on 
 Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the 
 first
 and the last C − α atoms of each chain were constrained.

 I wonder whether they used genrestr to restrain atoms, like 
 utilising -fc to add a quite large force in all directions to them, 
 and considered those atoms are kept fixed during NPT equilibration?


 People are often lazy (or inconsistent) with language.  Holding 
 something fixed might mean huge restraint or it might actually 
 mean frozen (freezegrps

Re: [gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear Justin,

I tried again, and the position restraint works well in NPT equilibration.

Thanks very much.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Friday, 19 June 2015 11:08 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation

Dear Justin,

I tried to equilibrate my collagen with all the heavy atoms restrained using 
define = -DPOSRES in NPT for 300 ps, but found that the collagen became much 
shorter. The restrained force for the heavy atoms generated through pdb2gmx is 
1000 kJ/mol/nm by default, why does the length changed a lot?

Thank you.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 18 June 2015 9:34 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation



On 6/18/15 6:28 AM, Ming Tang wrote:
 Dear Tsjerk and Justin,

 Thanks for your help. I have tried to use 1000 and 1 to restrained the 
 whole protein during NPT equilibration, but found the protein shape changed 
 as well. Is position restraint compatible with pressure coupling?


Restraints are compatible with pressure coupling.  Too high of a restraint can 
generate spurious forces, as Tsjerk mentioned below.  Note that restraints are 
just biasing potentials; they can allow for small changes in the structure.  
You shouldn't necessarily hike the force constant to some high value to try to 
absolutely fix the atoms.

-Justin

 Thanks very much.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Tsjerk Wassenaar
 Sent: Wednesday, 17 June 2015 1:53 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] confusion on NPT MD simulation

 Hi Ming Tang,

 You don't need a huge force constant to keep it fixed. Too high forces may 
 give instabilities. And a more gentle one (100-1000) does the trick as well.

 Cheers,

 Tsjerk
 On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear Justin,

 Thank you so much.  There are another 2 papers in which the authors 
 said they equilibrated their  collagen like this. This really made me 
 confused for quite a  long time, and I come to you for help finally.
 Critical analysis is important.

 In the steps to perform a simulation page, step 8  indicates that 
 NPT equilibration is for fixing the density. I have been confused 
 about how should I equilibrate my collagen before SMD simulation. I 
 want to keep the shape (do not change its length) of my collagen 
 during equilibration, so that the force-deformation curve will not be 
 changed because of the equilibration process. After knowing that 
 freezing and pressure coupling is incompatible, I tried to use NVT 
 with heavy atoms restrained by using -DPOSRES, and further the 
 simulation to SMD (actually umbrella and direction-periodic are used) 
 directly in NVT. The simulation run smoothly and I got my 
 force-deformation curve, but I am still concerned whether my 
 equilibration is good enough for SMD simulation, and whether the results are 
 credible.
 If I choose to further equilibrate my collagen in NPT after in NVT, 
 is it feasible to restrain parts (backbone, terminal atoms) of my 
 collagen by adding a huge force constant (say 1*10e6  kJ/mol/nm^2) 
 through -fc in genrestr command, so that its shape will be reserved 
 during the equilibration?

 Could you please kindly give me some guidance on which is the best 
 equilibration process I show follow to get a good starting point for 
 SMD
 (umbrella+direction-periodic) simulation?

 Thank you so much.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
 Justin Lemkul
 Sent: Tuesday, 16 June 2015 9:37 PM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] confusion on NPT MD simulation



 On 6/16/15 5:27 AM, Ming Tang wrote:
 Dear Justin,

 I read a paper, in which the author equilibrated the collagen like this:
 Firstly, a 100 ps NVT MD simulation at a temperature 310 K was 
 performed, in which velocity rescaling algorithm with 1ps coupling 
 constant was used. Rigid bonds were used to constraint covalent bond 
 length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble 
 with 1bar pressure was used to equilibrate the system while keeping 
 the temperature at 310 K, where Berendsen barostat with 1ps coupling 
 constant was adopted. In this step, the whole protein was held fixed.
 Lastly, we further equilibrated the system in a NPT ensemble for 
 400ps, with a more accurate pressure coupling algorithm based on 
 Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the 
 first
 and the last C − α atoms

Re: [gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear Tsjerk and Justin,

Thanks for your help. I have tried to use 1000 and 1 to restrained the 
whole protein during NPT equilibration, but found the protein shape changed as 
well. Is position restraint compatible with pressure coupling?

Thanks very much.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Wednesday, 17 June 2015 1:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] confusion on NPT MD simulation

Hi Ming Tang,

You don't need a huge force constant to keep it fixed. Too high forces may give 
instabilities. And a more gentle one (100-1000) does the trick as well.

Cheers,

Tsjerk
On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear Justin,

 Thank you so much.  There are another 2 papers in which the authors 
 said they equilibrated their  collagen like this. This really made me 
 confused for quite a  long time, and I come to you for help finally. 
 Critical analysis is important.

 In the steps to perform a simulation page, step 8  indicates that 
 NPT equilibration is for fixing the density. I have been confused 
 about how should I equilibrate my collagen before SMD simulation. I  
 want to keep the shape (do not change its length) of my collagen 
 during equilibration, so that the force-deformation curve will not be 
 changed because of the equilibration process. After knowing that 
 freezing and pressure coupling is incompatible, I tried to use NVT 
 with heavy atoms restrained by using -DPOSRES, and further the 
 simulation to SMD (actually umbrella and direction-periodic are used) 
 directly in NVT. The simulation run smoothly and I got my 
 force-deformation curve, but I am still concerned whether my 
 equilibration is good enough for SMD simulation, and whether the results are 
 credible.
 If I choose to further equilibrate my collagen in NPT after in NVT, is 
 it feasible to restrain parts (backbone, terminal atoms) of my 
 collagen by adding a huge force constant (say 1*10e6  kJ/mol/nm^2) 
 through -fc in genrestr command, so that its shape will be reserved 
 during the equilibration?

 Could you please kindly give me some guidance on which is the best 
 equilibration process I show follow to get a good starting point for 
 SMD
 (umbrella+direction-periodic) simulation?

 Thank you so much.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
 Lemkul
 Sent: Tuesday, 16 June 2015 9:37 PM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] confusion on NPT MD simulation



 On 6/16/15 5:27 AM, Ming Tang wrote:
  Dear Justin,
 
  I read a paper, in which the author equilibrated the collagen like this:
  Firstly, a 100 ps NVT MD simulation at a temperature 310 K was 
  performed, in which velocity rescaling algorithm with 1ps coupling 
  constant was used. Rigid bonds were used to constraint covalent bond 
  length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble 
  with 1bar pressure was used to equilibrate the system while keeping 
  the temperature at 310 K, where Berendsen barostat with 1ps coupling 
  constant was adopted. In this step, the whole protein was held fixed.
  Lastly, we further equilibrated the system in a NPT ensemble for 
  400ps, with a more accurate pressure coupling algorithm based on 
  Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the 
  first
 and the last C − α atoms of each chain were constrained.
 
  I wonder whether they used genrestr to restrain atoms, like 
  utilising -fc to add a quite large force in all directions to them, 
  and considered those atoms are kept fixed during NPT equilibration?
 

 People are often lazy (or inconsistent) with language.  Holding 
 something fixed might mean huge restraint or it might actually 
 mean frozen (freezegrps in the .mdp).  There are functional 
 differences between these two.  Atoms are also not constrained 
 (that's a restraint!) in GROMACS, so there may be some loose language here...

 If you have questions about methods for published work relevant to 
 what you're doing, that's what corresponding authors are for!

 -Justin

 --
 ==

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

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

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

 ==
 --
 Gromacs Users mailing list

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

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests

Re: [gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear Justin,

Thank you so much.  There are another 2 papers in which the authors said they 
equilibrated their  collagen like this. This really made me confused for quite 
a  long time, and I come to you for help finally. Critical analysis is 
important.

In the steps to perform a simulation page, step 8  indicates that NPT 
equilibration is for fixing the density. I have been confused about how should 
I equilibrate my collagen before SMD simulation. I  want to keep the shape (do 
not change its length) of my collagen during equilibration, so that the 
force-deformation curve will not be changed because of the equilibration 
process. After knowing that freezing and pressure coupling is incompatible, I 
tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the 
simulation to SMD (actually umbrella and direction-periodic are used) directly 
in NVT. The simulation run smoothly and I got my force-deformation curve, but I 
am still concerned whether my equilibration is good enough for SMD simulation, 
and whether the results are credible. 
If I choose to further equilibrate my collagen in NPT after in NVT, is it 
feasible to restrain parts (backbone, terminal atoms) of my collagen by adding 
a huge force constant (say 1*10e6  kJ/mol/nm^2) through -fc in genrestr 
command, so that its shape will be reserved during the equilibration?

Could you please kindly give me some guidance on which is the best 
equilibration process I show follow to get a good starting point for SMD 
(umbrella+direction-periodic) simulation?

Thank you so much.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Tuesday, 16 June 2015 9:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation



On 6/16/15 5:27 AM, Ming Tang wrote:
 Dear Justin,

 I read a paper, in which the author equilibrated the collagen like this:
 Firstly, a 100 ps NVT MD simulation at a temperature 310 K was 
 performed, in which velocity rescaling algorithm with 1ps coupling 
 constant was used. Rigid bonds were used to constraint covalent bond 
 length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble 
 with 1bar pressure was used to equilibrate the system while keeping 
 the temperature at 310 K, where Berendsen barostat with 1ps coupling 
 constant was adopted. In this step, the whole protein was held fixed. 
 Lastly, we further equilibrated the system in a NPT ensemble for 
 400ps, with a more accurate pressure coupling algorithm based on 
 Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and 
 the last C − α atoms of each chain were constrained.

 I wonder whether they used genrestr to restrain atoms, like utilising 
 -fc to add a quite large force in all directions to them, and 
 considered those atoms are kept fixed during NPT equilibration?


People are often lazy (or inconsistent) with language.  Holding something 
fixed might mean huge restraint or it might actually mean frozen 
(freezegrps in the .mdp).  There are functional differences between these two.  
Atoms are also not constrained (that's a restraint!) in GROMACS, so there may 
be some loose language here...

If you have questions about methods for published work relevant to what you're 
doing, that's what corresponding authors are for!

-Justin

--
==

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

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

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

==
--
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* Please search the archive at 
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Re: [gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear Justin,

I read a paper, in which the author equilibrated the collagen like this:
Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in 
which velocity rescaling algorithm with 1ps coupling constant was used.
Rigid bonds were used to constraint covalent bond length, allowing a time step 
of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to 
equilibrate the system while keeping the temperature at 310 K, where Berendsen 
barostat with 1ps coupling constant was adopted. In this step, the whole 
protein was held fixed. Lastly, we further equilibrated the system in a NPT 
ensemble for 400ps, with a more accurate pressure coupling algorithm based on 
Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the 
last C − α atoms of each chain were constrained.

I wonder whether they used genrestr to restrain atoms, like utilising -fc to 
add a quite large force in all directions to them, and considered those atoms 
are kept fixed during NPT equilibration?

Thanks in advance.



-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Monday, 15 June 2015 6:05 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation

Dear Justin,

I got a problem making me confused for weeks.
I found 2 journals, in which the author kept parts of their protein to 
equilibrate their system in NPT. Is there any other methods to keep atoms fixed 
during NPT equilibrium besides freezing them?
As you mentioned,  freezing and pressure coupling are incompatible. My first 
understanding was that I cannot fix atoms during NPT. Therefore, I have been 
steering my collagen in NVT recently.  After minimization, I equilibrated my 
collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, 
and then stretched it using pull code. Do you think this simple process can 
give a good starting point for SMD?

Thanks very much.

-Original Message-
From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.semailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 1 June 2015 9:46 PM
To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation



On 6/1/15 4:40 AM, Ming Tang wrote:
 Dear gromacs experts,

 I tried to equilibrate a triple helix using NPT, and the .mdp file is like 
 this:

 DEFINE   =  -DPOSRES
 integrator   =  md
 dt   =  0.0009
 nsteps   =  100
 nstxout  =  0
 nstvout  =  0
 nstlog   =  1
 nstxtcout=  1
 xtc-precision=  10
 cutoff-scheme=  verlet
 coulombtype  =  reaction-field-zero
 coulomb-modifier =  potential-shift-verlet rcoulomb-switch  =  0.8
 rcoulomb =  1.4
 epsilon_r=  15
 vdw-modifier =  force-switch
 rvdw-switch  =  0.8
 rvdw =  1.4
 tcoupl   =  v-rescale
 tc-grps  =  Protein non-protein
 tau-t=  1.0 1.0
 ref-t=  310 310
 Pcoupl   =  parrinello-Rahman
 Pcoupltype   =  isotropic
 tau-p=  5
 compressibility  =  3e-4
 ref-p=  1.0
 refcoord_scaling =  all
 pbc  =  xyz
 freezegrps   =  C
 freezedim=  Y Y Y

 C is a group containing atoms of both the first and the last residues in all 
 the three chains.
 But after 18ns' simulation, I found the one end of the triple helix moved. 
 Could you help to tell me whether this is normal or there is something wrong 
 with my simulation?
 Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that 
 both ends were fixed.  I need to keep the original geometry shape of the 
 triple helix, but berendsen algorithm is believed to be inaccurate.


Freezing and pressure coupling are incompatible; see notes in the manual.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear Justin,

I got a problem making me confused for weeks.
I found 2 journals, in which the author kept parts of their protein to 
equilibrate their system in NPT. Is there any other methods to keep atoms fixed 
during NPT equilibrium besides freezing them?
As you mentioned,  freezing and pressure coupling are incompatible. My first 
understanding was that I cannot fix atoms during NPT. Therefore, I have been 
steering my collagen in NVT recently.  After minimization, I equilibrated my 
collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, 
and then stretched it using pull code. Do you think this simple process can 
give a good starting point for SMD?

Thanks very much.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 1 June 2015 9:46 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation



On 6/1/15 4:40 AM, Ming Tang wrote:
 Dear gromacs experts,

 I tried to equilibrate a triple helix using NPT, and the .mdp file is like 
 this:

 DEFINE   =  -DPOSRES
 integrator   =  md
 dt   =  0.0009
 nsteps   =  100
 nstxout  =  0
 nstvout  =  0
 nstlog   =  1
 nstxtcout=  1
 xtc-precision=  10
 cutoff-scheme=  verlet
 coulombtype  =  reaction-field-zero
 coulomb-modifier =  potential-shift-verlet rcoulomb-switch  =  0.8
 rcoulomb =  1.4
 epsilon_r=  15
 vdw-modifier =  force-switch
 rvdw-switch  =  0.8
 rvdw =  1.4
 tcoupl   =  v-rescale
 tc-grps  =  Protein non-protein
 tau-t=  1.0 1.0
 ref-t=  310 310
 Pcoupl   =  parrinello-Rahman
 Pcoupltype   =  isotropic
 tau-p=  5
 compressibility  =  3e-4
 ref-p=  1.0
 refcoord_scaling =  all
 pbc  =  xyz
 freezegrps   =  C
 freezedim=  Y Y Y

 C is a group containing atoms of both the first and the last residues in all 
 the three chains.
 But after 18ns' simulation, I found the one end of the triple helix moved. 
 Could you help to tell me whether this is normal or there is something wrong 
 with my simulation?
 Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that 
 both ends were fixed.  I need to keep the original geometry shape of the 
 triple helix, but berendsen algorithm is believed to be inaccurate.


Freezing and pressure coupling are incompatible; see notes in the manual.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] g_wham error in umbrella simulation

[Ming Tang]

Hi，高
发银行卡号给我，我还你钱，你结婚肯定要用钱吧

Sent from my Huawei Mobile

Ming Tang m21.t...@qut.edu.au wrote:

Dear all,

I am doing an umbrella simulation, and come across the following error.

Command line:
  g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000

Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, 
respectively
Reading 13 tpr and pullf files
Automatic determination of boundaries...

---
Program g_wham, VERSION 5.0.4
Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, 
line: 1767

Fatal error:
. Should be tpr, xvg, or pdo.0.tpr

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

tpr-files.dat:
umbrella0.tpr
umbrella137.tpr
umbrella155.tpr
umbrella163.tpr
umbrella169.tpr
umbrella174.tpr
umbrella179.tpr
umbrella185.tpr
umbrella199.tpr
umbrella206.tpr
umbrella223.tpr
umbrella239.tpr
umbrella257.tpr
umbrella275.tpr
umbrella291.tpr
umbrella308.tpr
umbrella324.tpr
umbrella344.tpr
umbrella369.tpr
umbrella383.tpr
umbrella392.tpr
umbrella422.tpr
umbrella450.tpr
umbrella463.tpr
umbrella479.tpr
umbrella497.tpr
umbrella499.tpr

pullf-files.dat
pullf0.xvg
pullf137.xvg
pullf155.xvg
pullf163.xvg
pullf169.xvg
pullf174.xvg
pullf179.xvg
pullf185.xvg
pullf199.xvg
pullf206.xvg
pullf223.xvg
pullf239.xvg
pullf257.xvg
pullf275.xvg
pullf291.xvg
pullf308.xvg
pullf324.xvg
pullf344.xvg
pullf369.xvg
pullf383.xvg
pullf392.xvg
pullf422.xvg
pullf450.xvg
pullf463.xvg
pullf479.xvg
pullf497.xvg
pullf499.xvg

I used this method several times before, and did not come across this problem. 
could anybody tell me where is the problem?
Thanks

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Re: [gmx-users] gmx distance

[Ming Tang]

Dear Justin,

I have invited you to share the dist.xvg, please help to have a look. I cannot 
understand why does the distance between two ends start at around -4nm. In 
distance.mdp, I set pull rate to be 0.001nm/ps. After pulling 30ns, the COM 
distance should increase 30nm. Am I right? But the length of the helix aslo 
shows only a 15nm increase (see len-ahx.xvg). Another thing is, why does the 
length of the helix jump from 5ns to 10ns?  I found that the pullf.xvg records 
the force for every step, making it too large to be processed by excel. Is 
there any method that I can use to extract the pull force with specific time 
interval like using gmx distance -dt to get distance? 

Thanks very much.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Sunday, 7 June 2015 11:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx distance



On 6/5/15 9:49 PM, Ming Tang wrote:
 Thanks, Justin

 Using -pbc or not gives the same curve. I tried to guess the curve give the 
 deviation of the two end groups, but the curve drops from around 4nm to 1nm 
 at the beginning. I am really confused about this.


Without seeing the plots and the index groups, there's nothing I can guess.

-Justin

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Justin Lemkul
 Sent: Saturday, 6 June 2015 2:56 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] gmx distance



 On 6/5/15 7:07 AM, Ming Tang wrote:
 Dear gromacs experts,

 I am stretching a triple helix along z direction by fixing one end 
 and pull the other. The helix length changes from 35nm to 50nm during the MD 
 simulation. However, after using gmx distance -n index.ndx -f traj.trr -s 
 topol.tpr -select 'com of group start plus com of group end' -oav dist.xvg
 to get the distance between the two end groups,   I found that the distance 
 varies from 2nm to 15nm during the simulation.
 I am quite confused about this, because the original length of the helix is 
 around 35nm. The configuration looks correct
 Am I wrong when using gmx distance?


 Probably -pbc is relevant here.

-[no]pbc(yes)
Use periodic boundary conditions for distance calculation

 You're likely getting the inter-image distance rather than the one within the 
 unit cell.

 -Justin

 --
 ==

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

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

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

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

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 mail to gmx-users-requ...@gromacs.org.


--
==

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

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

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

==
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[gmx-users] gmx distance

[Ming Tang]

Dear gromacs experts,

I am stretching a triple helix along z direction by fixing one end and pull the 
other. The helix length changes from 35nm to 50nm during the MD simulation. 
However, after using
gmx distance -n index.ndx -f traj.trr -s topol.tpr -select 'com of group start 
plus com of group end' -oav dist.xvg
to get the distance between the two end groups,   I found that the distance 
varies from 2nm to 15nm during the simulation.
I am quite confused about this, because the original length of the helix is 
around 35nm. The configuration looks correct
Am I wrong when using gmx distance?

Thanks in advance.

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[gmx-users] g_helix issue

[Ming Tang]

Dear all,

I am using gromos54a7 ff to simulate a triple helix. When using g_helix to get 
some of the basic properties, I got the following error:

Program g_helix, VERSION 5.0.4
Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/hxprops.c, 
line: 437

Fatal error:
Zero complete backbone residues were found, cannot proceed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Could anybody tell me how to fix this problem?

Thanks.
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Re: [gmx-users] fix COM of a group

[Ming Tang]

Dear Tsjerk,

Yes, you are right. I want to fix the COM of the reference group (one end of a 
triple helix), and pull the other end. I tried to freeze the reference group, 
but found this setting restricted the unfolding process of my triple helix. 
That's why I want to find a way to fix the COM only.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Wednesday, 3 June 2015 11:18 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] fix COM of a group

Hi Ming Tang,

You didn't tell you were pulling... That's a totally different matter. I guess 
you want to use two pull groups and pull one with respect to the other.

Cheers,

Tsjerk

On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear Tsjerk,

 Thanks for your guidance. I add those two command lines you gave in 
 .mdp, but got the following warnings.

 WARNING 1 [file dynamic.mdp]:
   Some atoms are not part of any center of mass motion removal group.
   This may lead to artifacts.
   In most cases one should use one group for the whole system.

 Number of degrees of freedom in T-Coupling group Protein is 8680.88 
 Number of degrees of freedom in T-Coupling group non-Protein is 
 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps 
 at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer 
 size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, 
 buffer size 0.000 nm

 WARNING 2 [file dynamic.mdp]:
   You are using an absolute reference for pulling, but the rest of the
   system does not have an absolute reference. This will lead to artifacts.

 Pull group  natoms  pbc atom  distance at start  reference at t=0
0 0 0
1 3  1919  -1.542 nm -1.542 nm

 Can I just ignore them?
 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Wednesday, 3 June 2015 5:41 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] fix COM of a group

 Hi Ming Tang,

 comm_mode = Linear
 comm_grps = CA

 Cheers,

 Tsjerk

 On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote:

  Dear all,
 
  Is there any method that can fix the center of mass of a group of 
  atoms? I create a group containing CA atoms of the first residue in 
  each of the three chains, and want to fix its center of mass only 
  without freeze the CA atoms.
 
  Thanks.
  --
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  posting!
 
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 --
 Tsjerk A. Wassenaar, Ph.D.
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--
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] fix COM of a group

[Ming Tang]

Dear Tsjerk,

Thanks for your guidance. I add those two command lines you gave in .mdp, but 
got the following warnings.

WARNING 1 [file dynamic.mdp]:
  Some atoms are not part of any center of mass motion removal group.
  This may lead to artifacts.
  In most cases one should use one group for the whole system.

Number of degrees of freedom in T-Coupling group Protein is 8680.88
Number of degrees of freedom in T-Coupling group non-Protein is 202734.12
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm

WARNING 2 [file dynamic.mdp]:
  You are using an absolute reference for pulling, but the rest of the
  system does not have an absolute reference. This will lead to artifacts.

Pull group  natoms  pbc atom  distance at start  reference at t=0
   0 0 0
   1 3  1919  -1.542 nm -1.542 nm

Can I just ignore them? 
Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Wednesday, 3 June 2015 5:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] fix COM of a group

Hi Ming Tang,

comm_mode = Linear
comm_grps = CA

Cheers,

Tsjerk

On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear all,

 Is there any method that can fix the center of mass of a group of 
 atoms? I create a group containing CA atoms of the first residue in 
 each of the three chains, and want to fix its center of mass only 
 without freeze the CA atoms.

 Thanks.
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[gmx-users] fix COM of a group

[Ming Tang]

Dear all,

Is there any method that can fix the center of mass of a group of atoms? I 
create a group containing CA atoms of the first residue in each of the three 
chains, and want to fix its center of mass only without freeze the CA atoms.

Thanks.
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[gmx-users] does gromos force field support implicit solvent?

[Ming Tang]

Dear gromacs experts,

I tried to  use gromos 54a7 force field to calculate persistence length of a 
helix in implicit solvent, but got GB parameters missing errors. When I tried 
to modify the implicit_genborn_params section, I found there is not gbsa.itp 
file in gromos54a7.ff
does gromos force field support implicit solvent calculation?

Thanks.
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[gmx-users] confusion on NPT MD simulation

[Ming Tang]

Dear gromacs experts,

I tried to equilibrate a triple helix using NPT, and the .mdp file is like this:

DEFINE   =  -DPOSRES
integrator   =  md
dt   =  0.0009
nsteps   =  100
nstxout  =  0
nstvout  =  0
nstlog   =  1
nstxtcout=  1
xtc-precision=  10
cutoff-scheme=  verlet
coulombtype  =  reaction-field-zero
coulomb-modifier =  potential-shift-verlet
rcoulomb-switch  =  0.8
rcoulomb =  1.4
epsilon_r=  15
vdw-modifier =  force-switch
rvdw-switch  =  0.8
rvdw =  1.4
tcoupl   =  v-rescale
tc-grps  =  Protein non-protein
tau-t=  1.0 1.0
ref-t=  310 310
Pcoupl   =  parrinello-Rahman
Pcoupltype   =  isotropic
tau-p=  5
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  all
pbc  =  xyz
freezegrps   =  C
freezedim=  Y Y Y

C is a group containing atoms of both the first and the last residues in all 
the three chains.
But after 18ns' simulation, I found the one end of the triple helix moved. 
Could you help to tell me whether this is normal or there is something wrong 
with my simulation?
Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that 
both ends were fixed.  I need to keep the original geometry shape of the triple 
helix, but berendsen algorithm is believed to be inaccurate.

Thanks.
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[gmx-users] persistence length of triple helix

[Ming Tang]

Dear all,

I want to calculate the persistence length of a triple helix. After 
minimization and equilibration, I did MD simulation without position restraints 
for atoms.
I read the second paragraph of gmx polystat, and understood that for one chain, 
I can choose its backbone atoms as the index group and got the persistence 
length. In the description, the persistence length is defined as number of 
bonds. Can I understand it as the persistence length equals to the number of 
bonds multiply the bond length? But how can I determine the bond length?

For the triple helix, I think I need to work with the centre of mass of the 
three backbone atoms in the three chains.  The three chains in the triple helix 
are identical. How can I get the trajectory of the centre of mass of the same 
backbone atoms(or alpha carbon atoms) in the three different chains? And after 
getting this trajectory, can I use gmx gangle to calculate the angles and then 
calculate their cosine values and finally get its persistence length?  But how 
to determine the index file? I want to calculate the angle between every third 
point of centre of mass.  Could anyone help to give me some guidance about how 
to do this?

Thanks in advance.
regards
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Re: [gmx-users] first residue in chains warning issue

[Ming Tang]

Thanks, Justin

For a stable system, is it true that it can be equilibrated endlessly without 
error?   I got LINCS errors when my protein had been equilibrated for about 
50ns. Does this mean that there is some wrong with my system?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Saturday, 23 May 2015 6:24 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue



On 5/22/15 3:39 AM, Ming Tang wrote:

 Dear Justin,

 Is there any significant difference between the equilibrated states of the 
 protein equilibrated by NPT with all-bonds constrained and without any 
 constraints?
 If the difference is quite small, then I can choose constraining bonds to 
 increase time step.


This is generally (read: pretty much always) what people do in biomolecular 
simulations.  The bonds are rarely (read: practically never) excited from their 
ground state, so constraints are a reasonable approximation.  This isn't 
universal, but it's definitely true in most biological systems at ambient 
conditions.

-Justin

--
==

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

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

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

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Re: [gmx-users] first residue in chains warning issue

[Ming Tang]

Dear Justin,

Is there any significant difference between the equilibrated states of the 
protein equilibrated by NPT with all-bonds constrained and without any 
constraints?
If the difference is quite small, then I can choose constraining bonds to 
increase time step.

Thanks a lot.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 18 May 2015 9:44 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue



On 5/18/15 7:39 AM, Ming Tang wrote:
 Dear Justin,

 After minimization, I got the following note when using NPT.

 NOTE 1 [file topol.top, line 49]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has 
 an estimated oscillational period of 1.0e-02 ps, which is less than 10
times the time step of 1.0e-03 ps.  Maybe you forgot to change the 
 constraints mdp option.

 Does this has something to do with the warning given by pdb2gmx?
 When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there 
 anything wrong with my topol.top?


No, as the note says, you probably aren't using constraints, which if you want 
a 1-fs or larger value of dt, you need to be using.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] water box moves during MD simulation

[Ming Tang]

Dear Mark,

Thanks a lot. 
Is it possible to get the water box fixed through command in .mdp, or using a 
specific option to fix the water box, like -nojump for g_traj?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Wednesday, 20 May 2015 7:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water box moves during MD simulation

Hi,

You can add (say) -1.23 to every x coordinate and you have a description of the 
same system. So you can pick any of these for doing the simulation, and any of 
these for representing the trajectory afterwards.

Mark

On Wed, May 20, 2015 at 11:19 AM Ming Tang m21.t...@qut.edu.au wrote:

 Dear Brother，

 What does Mark mean？

 Sent from my Huawei Mobile

 Mark Abraham mark.j.abra...@gmail.com wrote:

 Hi,

 Nothing wrong with the .mdp file. But you should check your assumption 
 that there's a single meaningful location where an infinite periodic 
 system should be located :-) There's lots of equivalent 
 representations, so mdrun suits itself.

 Mark

 On Wed, May 20, 2015 at 9:05 AM Ming Tang m21.t...@qut.edu.au wrote:

  Dear all,
 
  After MD dynamic simulation for 100 ps, I found the water box was 
  moving during the simulation, but my protein was inside the water 
  box all the
 time.
  Here is the . mdp file I used:
 
  integrator   =  md
  dt   =  0.001
  nsteps   =  10
  nstxout  =  1000
  nstvout  =  1000
  nstlog   =  1000
  nstxout-compressed=  100
  xtc-precision=  10
  cutoff-scheme=verlet
  rlist=  1.4
  coulombtype  = reaction-field-zero
  coulomb-modifier = potential-shift-verlet rcoulomb-switch  =  0.8
  rcoulomb =  1.4
  epsilon_r=  15
  vdw-modifier =  potential-switch
  rvdw-switch  =  0.8
  rvdw =  1.4
  tcoupl   =  v-rescale
  tc-grps  =  Protein non-protein
  tau-t=  1.0 1.0
  ref-t=  300 300
  Pcoupl   =  parrinello-rahman
  Pcoupltype   =  isotropic
  tau-p=  12.0
  compressibility  =  3e-4
  ref-p=  1.0
  refcoord_scaling =  all
  pbc  =  xyz
  constraints  = h-bonds
 
  Could anybody tell me what's wrong with my .mdp file?
 
  Thanks in advance.
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Re: [gmx-users] Pull code

[Ming Tang]

Dear Justin,

I want to simulate my triple helix using SMD, Can I use umbrella + distance?  I 
saw many people doing SMD simulation by fixing one end and pull another end in 
their journal. Besides, my triple helix deviates a bit from Z axis, but I do 
not know the angle. I checked both dim for distance and pull-vec for direction, 
and found both of them needs pull direction. If I set dim = N N Y, will the 
force-deformation be reliable?

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 23 April 2015 10:33 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pull code



On 4/22/15 8:03 PM, Ming Tang wrote:
 Hi, Justin

 I am confusing about what is the difference between the rigid constraint in 
 constraint pull method and the harmonic potential using umbrella.
 The force acts directly on the centre of mass of the group in constraint, and 
 the force acts on the center of mass of the group through a spring when using 
 umbrella pull method.
 Am I right?

There is of course no difference in the fact that the two groups are restrained 
between their COM.  The difference comes in how the force is applied and how 
the positions are updated.  It's just like bonds.  A harmonic bond (connection, 
restraint, whatever) oscillates about some mean value.  That's the deal with 
the umbrella harmonic restraint.  There is a target value, and the deviation 
from that target determines the magnitude of the force applied along the 
restraint vector to give rise to that target.  With the constraint method, 
the positions are updated with SHAKE (as stated in the manual).  A difference 
vector is calculated between the current position and the target position.  The 
positions of the groups are then updated along that vector such that the rigid 
constraint is satisfied.  It's the difference between being connected with a 
spring and being connected with a lead pipe.

-Justin


 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Justin Lemkul
 Sent: Thursday, 23 April 2015 9:22 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] Pull code



 On 4/22/15 7:17 PM, Ming Tang wrote:
 Hi，Alex

 You can try constraint. In umbrella， both 2 groups move.


 Not really.  The constraint option keeps a rigid constraint between the two 
 groups.  The umbrella keyword specifies a harmonic potential, whose 
 strength is tunable.  Otherwise, the two methods are identical.

 If one group needs to stay in place, it needs position restraints applied to 
 it.
If the desired separation is not occurring, either a larger spring force 
 constant or a faster pull rate is needed.

 -Justin

 Sent from my Huawei Mobile

 Alex nedoma...@gmail.com wrote:

 Hi all,

 I have a group (DNA) I'd like to translate relative to the other 
 group
 (CNT) along the Z-direction so that DNA is the only group that's 
 actually moving.

 The code I had prior to what I have now worked under GMX 4.5.something.
 Since the syntax has changed in 5.0.x, I found Justin's old 
 suggestions, and this is what I have now:

 ;Pull code

 pull= umbrella

 pull_geometry   = direction

 pull_coord1_vec = 0.0 0.0 1.0

 pull_start  = yes

 pull_coord1_init= 0.0

 pull_ngroups= 2

 pull_ncoords= 1

 pull_coord1_groups  = 1 2

 pull_group1_name= CNT

 pull_group2_name= DNA

 pull_coord1_rate1   = 0.0002  ;nm per ps

 pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2

 ;end pull code


 Does this look right? My simulation isn't nearly done, but I am 
 looking at the Z-displacement in pullx.xvg and it just oscillates 
 around a single value. The simulated time is now about 1.5 ns.


 Thank you,


 Alex
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 --
 ==

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

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

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

 ==
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[gmx-users] distance constrain of two groups

[Ming Tang]

Dear all,

After energy minimization, I want to equilibrate my triple helix using NPT, but 
need to keep its general shape, as I want to study the load-deformation 
relationship including the triple helix unfolding stage. During the 
equilibration, I want to fix the distance between the centre of mass of two 
group atoms  along the vector connecting the two groups.
Could anybody tell me how can I do this？

Thanks in advance.


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[gmx-users] water box moves during MD simulation

[Ming Tang]

Dear all,

After MD dynamic simulation for 100 ps, I found the water box was moving during 
the simulation, but my protein was inside the water box all the time.
Here is the . mdp file I used:

integrator   =  md
dt   =  0.001
nsteps   =  10
nstxout  =  1000
nstvout  =  1000
nstlog   =  1000
nstxout-compressed=  100
xtc-precision=  10
cutoff-scheme=verlet
rlist=  1.4
coulombtype  = reaction-field-zero
coulomb-modifier = potential-shift-verlet
rcoulomb-switch  =  0.8
rcoulomb =  1.4
epsilon_r=  15
vdw-modifier =  potential-switch
rvdw-switch  =  0.8
rvdw =  1.4
tcoupl   =  v-rescale
tc-grps  =  Protein non-protein
tau-t=  1.0 1.0
ref-t=  300 300
Pcoupl   =  parrinello-rahman
Pcoupltype   =  isotropic
tau-p=  12.0
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  all
pbc  =  xyz
constraints  = h-bonds

Could anybody tell me what's wrong with my .mdp file?

Thanks in advance.
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Re: [gmx-users] water box moves during MD simulation

[Ming Tang]

Dear Brother，

What does Mark mean？

Sent from my Huawei Mobile

Mark Abraham mark.j.abra...@gmail.com wrote:

Hi,

Nothing wrong with the .mdp file. But you should check your assumption that
there's a single meaningful location where an infinite periodic system
should be located :-) There's lots of equivalent representations, so mdrun
suits itself.

Mark

On Wed, May 20, 2015 at 9:05 AM Ming Tang m21.t...@qut.edu.au wrote:

 Dear all,

 After MD dynamic simulation for 100 ps, I found the water box was moving
 during the simulation, but my protein was inside the water box all the time.
 Here is the . mdp file I used:

 integrator   =  md
 dt   =  0.001
 nsteps   =  10
 nstxout  =  1000
 nstvout  =  1000
 nstlog   =  1000
 nstxout-compressed=  100
 xtc-precision=  10
 cutoff-scheme=verlet
 rlist=  1.4
 coulombtype  = reaction-field-zero
 coulomb-modifier = potential-shift-verlet
 rcoulomb-switch  =  0.8
 rcoulomb =  1.4
 epsilon_r=  15
 vdw-modifier =  potential-switch
 rvdw-switch  =  0.8
 rvdw =  1.4
 tcoupl   =  v-rescale
 tc-grps  =  Protein non-protein
 tau-t=  1.0 1.0
 ref-t=  300 300
 Pcoupl   =  parrinello-rahman
 Pcoupltype   =  isotropic
 tau-p=  12.0
 compressibility  =  3e-4
 ref-p=  1.0
 refcoord_scaling =  all
 pbc  =  xyz
 constraints  = h-bonds

 Could anybody tell me what's wrong with my .mdp file?

 Thanks in advance.
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Re: [gmx-users] first residue in chains warning issue

[Ming Tang]

Hi Justin,

Do you mean options for bonds or something like fix and pull atoms?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 18 May 2015 9:44 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue



On 5/18/15 7:39 AM, Ming Tang wrote:
 Dear Justin,

 After minimization, I got the following note when using NPT.

 NOTE 1 [file topol.top, line 49]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has 
 an estimated oscillational period of 1.0e-02 ps, which is less than 10
times the time step of 1.0e-03 ps.  Maybe you forgot to change the 
 constraints mdp option.

 Does this has something to do with the warning given by pdb2gmx?
 When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there 
 anything wrong with my topol.top?


No, as the note says, you probably aren't using constraints, which if you want 
a 1-fs or larger value of dt, you need to be using.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

I just tried, but it stopped for too many LICS warnings at step 6000. Small 
triple helix can be equilibrated for 1000ns with NPT.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino 
 acids per chain(generated simply by deleting other atoms in .pdb file 
 of the real triple helix) can be equilibrated for 1ns using exactly 
 the same control files, and the real triple helix can be used for full 
 atomic simulation without any problem. The CG topology is generated 
 using the same mitinize.py downloaded from the website. I will try for 
 another time, and will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after 
  running
 20ps, I found one chain of the triple helix just went to another water 
 box totally. I guess there is something wrong with the martini ff 
 because of the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the 
  .gro,
 and found all the three chains stay together, which is reasonable. 
 However, even use dt=0.01, the simulation can only run about 1ns. And, 
 after simulating 100 ps using dt=0.01ps, the simulation can just run 
 thousands of steps when dt is increased to 0.02ps. I tried many times 
 and many different time steps, but still could not see the possibility 
 for it to run hundreds of  nanoseconds, which is quite normal when 
 using martini force. If the system can be further minimized, then it can run 
 longer maybe.
 

 This seems entirely random and suggests instead that there is 
 something simply physically unstable with the system or problematic in the 
 topology.
 I don't use MARTINI (or CG models in general) so there's little else I 
 can suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a 
 PBC effect and not a true dissociation.  If it is a dissociation, it's 
 not simply because of the time step.

 -Justin

 --
 ==

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

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

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

 ==
 --
 Gromacs Users mailing list

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

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Re: [gmx-users] energy minimization problem

[Ming Tang]

Thanks a lot, Justin

It really makes me feel weird. The small triple helix with 30 amino acids per 
chain(generated simply by deleting other atoms in .pdb file of the real triple 
helix) can be equilibrated for 1ns using exactly the same control files, and 
the real triple helix can be used for full atomic simulation without any 
problem. The CG topology is generated using the same mitinize.py downloaded 
from the website. I will try for another time, and will tell you if I fix it.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Sunday, 17 May 2015 7:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/16/15 8:30 AM, Ming Tang wrote:
 Dear Justin,

 I tried to use small time step. First,  set dt=0.005ps, after running 20ps, I 
 found one chain of the triple helix just went to another water box totally. I 
 guess there is something wrong with the martini ff because of the small time 
 step.
 Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and 
 found all the three chains stay together, which is reasonable. However, even 
 use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 
 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is 
 increased to 0.02ps. I tried many times and many different time steps, but 
 still could not see the possibility for it to run hundreds of  nanoseconds, 
 which is quite normal when using martini force. If the system can be further 
 minimized, then it can run longer maybe.


This seems entirely random and suggests instead that there is something simply 
physically unstable with the system or problematic in the topology.  I don't 
use MARTINI (or CG models in general) so there's little else I can suggest.  
Maybe someone more experienced with such systems will chime in.

Also note that a chain moving into another box is probably just a PBC effect 
and not a true dissociation.  If it is a dissociation, it's not simply because 
of the time step.

-Justin

--
==

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

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

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

==
--
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr
mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website. 
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation, 
  it's not simply because of the time step.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences School of Pharmacy Health 
  Sciences Facility II, Room 629 University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441 
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe

Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website.
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation, 
  it's not simply because of the time step.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences School of Pharmacy Health 
  Sciences Facility II, Room 629 University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441 
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
  posting!
 
  * Can't post? Read http

Re: [gmx-users] energy minimization problem

[Ming Tang]

Besides, the martini.itp does not contain  moleculetype CL, so I edit it like 
this:

[ moleculetype ]
; molname   nrexcl
  CL1

[ atoms ]
;id typeresnr   residu  atomcgnrcharge
 1  P4  1   CL  CL  1   -1

Please help to have a look. I do not know whether it is true or not, as the 
small triple helix used for test does not carry charge, so I did not add CL.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Monday, 18 May 2015 7:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem




Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website.
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation

Re: [gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

This protein has a total charge of 35e, and I added 35 CL to balance the 
system. Is there any difference between adding CL and not adding CL?
Thank you.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino 
 acids per chain(generated simply by deleting other atoms in .pdb file 
 of the real triple helix) can be equilibrated for 1ns using exactly 
 the same control files, and the real triple helix can be used for full 
 atomic simulation without any problem. The CG topology is generated 
 using the same mitinize.py downloaded from the website. I will try for 
 another time, and will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after 
  running
 20ps, I found one chain of the triple helix just went to another water 
 box totally. I guess there is something wrong with the martini ff 
 because of the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the 
  .gro,
 and found all the three chains stay together, which is reasonable. 
 However, even use dt=0.01, the simulation can only run about 1ns. And, 
 after simulating 100 ps using dt=0.01ps, the simulation can just run 
 thousands of steps when dt is increased to 0.02ps. I tried many times 
 and many different time steps, but still could not see the possibility 
 for it to run hundreds of  nanoseconds, which is quite normal when 
 using martini force. If the system can be further minimized, then it can run 
 longer maybe.
 

 This seems entirely random and suggests instead that there is 
 something simply physically unstable with the system or problematic in the 
 topology.
 I don't use MARTINI (or CG models in general) so there's little else I 
 can suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a 
 PBC effect and not a true dissociation.  If it is a dissociation, it's 
 not simply because of the time step.

 -Justin

 --
 ==

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

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

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

 ==
 --
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Re: [gmx-users] first residue in chains warning issue

[Ming Tang]

Dear Justin,

After minimization, I got the following note when using NPT.

NOTE 1 [file topol.top, line 49]:
  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an 
estimated oscillational period of 1.0e-02 ps, which is less than 10
  times the time step of 1.0e-03 ps.  Maybe you forgot to change the 
constraints mdp option.

Does this has something to do with the warning given by pdb2gmx?
When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything 
wrong with my topol.top? 

Thanks.


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Tuesday, 12 May 2015 10:19 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue



On 5/12/15 8:10 AM, Ming Tang wrote:

 Thanks Justin,

 At first, I wanted to choose NONE in for both N and C terminus, but it gave 
 me the same warnings for both the first and the last residue in every chains. 
 However, choose NH3+/COO- and NH2/COOH just gave that warning for the first 
 residue.


Right, because choosing None is chemical nonsense in this context.

 The angles and bonds in .itp are like this:

 [ bonds ]
 ;  aiaj functc0c1c2c3
  1 2 2gb_2
  1 3 2gb_2
  1 4 2gb_21
  4 5 2gb_27

 [ angles ]
 ;  aiajak functc0c1c2
 c3
  2 1 3 2ga_10
  2 1 4 2ga_10
  2 1 5 2ga_11
  3 1 4 2ga_10
  3 1 5 2ga_11
  4 1 5 2ga_11
  1 5 6 2ga_13
  1 513 2ga_13
  6 513 2ga_13

 Just now, I tried to delete one H atom of the first residue in the input 
 .pdb, but got the same warnings for them. Is there  anything wrong with the 
 angle and bond?

Well, cross-reference what the atoms are and what the parameters should be. 
That's your job, not mine :)  Energy minimization and a quick MD run will show 
you if there are any problems; if things are missing or wrong (very unlikely, 
but always check when you see warnings!) then the structure will be obviously 
wrong very quickly.  Like I said, this is really most likely just some weird 
case in the code that isn't handled elegantly, but there's not enough to go on 
for a full debug.

-Justin

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Justin Lemkul
 Sent: Tuesday, 12 May 2015 9:35 PM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] first residue in chains warning issue



 On 5/11/15 6:48 PM, Ming Tang wrote:
 Hi Justin,

 Here is the output of pdb2gmx:

 Command line:
 pdb2gmx -f hyp_lys.pdb -o complex.gro -ignh -ter -ff gromos54a7 
 -water SPC


 Using the Gromos54a7 force field in directory gromos54a7.ff

 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
 Reading hyp_lys.pdb...
 Read 20130 atoms
 Analyzing pdb file
 Splitting chemical chains based on TER records or chain id changing.
 There are 3 chains and 0 blocks of water and 3134 residues with 20130 
 atoms

 chain  #res #atoms
 1 'A'  1054   6788
 2 'B'  1026   6554
 3 'C'  1054   6788

 All occupancies are one
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
 Atomtype 58
 Reading residue database... (gromos54a7) Opening force field file 
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
 Using default: not generating all possible dihedrals Using default:
 excluding 3 bonded neighbors Using default: generating 1,4 H--H 
 interactions Using default: removing proper dihedrals found on the 
 same bond as a proper dihedral Residue 108 Sorting it all out...
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb

 Back Off! I just backed up topol.top to ./#topol.top.2# Processing 
 chain 1 'A' (6788 atoms, 1054 residues) Analysing hydrogen-bonding 
 network for automated assignment of histidine
protonation. 1365 donors and 1444 acceptors were found.
 There are 1748 hydrogen bonds
 Will use HISE for residue 105
 Will use HISE for residue 948
 Identified residue GLN1 as a starting terminus.
 Identified residue TYR1054 as a ending terminus.
 8 out of 8 lines of specbond.dat converted successfully Special Atom 
 Distance matrix:
   MET2   MET19   MET55  MET102  HIS105  MET139  MET418
   SD15   SD136   SD369   SD678  NE2702   SD926  SD2692
  MET19

Re: [gmx-users] energy minimization problem

[Ming Tang]

Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be 
reasonable according to gromacs website. So ijust kept trying 0.02ps

Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 5/14/15 10:02 PM, Ming Tang wrote:
 Hi Justin

 Here is the .mdp file with position restraints, which I downloaded from the 
 martini tutorial website. It works well with the tutorial and my small triple 
 helix, and the grompp process does not give any warnings. Please help to have 
 a look. Many thanks to you.

 define   =  -DPOSRES
 integrator   =  md
 dt   =  0.02

Have you tried simply reducing the time step?  20 fs may be reasonable for a
well equilibrated system, but if the run is dying early, then this is the first
thing I would look at.

-Justin

 nsteps   =  5
 nstxout  =  0
 nstvout  =  0
 nstlog   =  1000
 nstxtcout=  1000
 xtc-precision=  10
 cutoff-scheme=verlet
 coulombtype  = reaction-field-zero
 coulomb-modifier = potential-shift-verlet
 rcoulomb-switch  =  0.9
 rcoulomb =  1.4
 epsilon_r=  15
 vdw-modifier =  force-switch
 rvdw-switch  =  0.9
 rvdw =  1.4
 tcoupl   =  v-rescale
 tc-grps  =  Protein W
 tau-t=  1.0 1.0
 ref-t=  310 310
 compressibility  =  3e-4
 ref-p=  1.0
 refcoord_scaling =  all
 pbc  =  xyz

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
 Justin Lemkul
 Sent: Friday, 15 May 2015 11:50 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/14/15 9:47 PM, Ming Tang wrote:
 Dear Justin,

 I saw it in the terminal.

 Potential Energy  = -6.3682131e+05
 Maximum force =  1.8876091e+02 on atom 1147
 Norm of force =  3.1155257e+00

 But, how can I further minimize my protein?


 Minimization is not your problem.  Post a full .mdp file of the run that is 
 failing.

 -Justin

 --
 ==

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

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

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

 ==
 --
 Gromacs Users mailing list

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

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
 mail to gmx-users-requ...@gromacs.org.


--
==

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

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

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

==
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Re: [gmx-users] energy minimization problem

[Ming Tang]

Dear Justin,

could you please tell me how to get the maximum force of an exact atom? I tried 
g_traj -of, but did not get any force data.
Thanks a lot.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Friday, 15 May 2015 2:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/14/15 3:12 AM, Ming Tang wrote:
 Dear all,

 I am working with a triple helix containing around 1000 amino acids per chain 
 using martini force field. After energy minimization until it cannot be 
 minimized any more, I moved to NPT, but got LINCS error after thousands of 
 steps. Following Justin's advice on LINCS error, I checked all of the 
 possible causes in blowing up page, but still did not find the reason. Later, 
 I created a smaller model including 30 amino acids per chain, and found it 
 could be move forward to dynamic simulation smoothly using the same control 
 files. Does this mean that my control files are ok?
 I noticed that the minimization was not good enough when working with my real 
 triple helix, as it got stuck in a certain atom (Epot does not change). I 
 have tried to change to use cg algorithm, but got no improvement. Could 
 anybody tell me how to further minimize my triple helix. I got stuck here for 
 3 days.


Sounds like your initial geometry is just bad.  Inspect the surroundings of the 
atom with maximum force; that usually gives an indication of what's going on.

-Justin

--
==

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

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

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

==
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[gmx-users] martini issues

[Ming Tang]

Dear all,


I am learning martini method in gromacs through the tutorial 
http://md.chem.rug.nl/cgmartini/index.php/proteins.http://md.chem.rug.nl/cgmartini/index.php/proteins
 when solvating the system, I came across the following note:

NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be removed 
in a future release when 'verlet' supports all interaction forms.

right now, i am using water-box-CG_301K-1bar.gro, which I downloaded from that 
tutorial website. could anybody tell me where i can get the CG water model 
suitable for verlet cutoff-scheme?

Aslo, I got the following warning when doing gmx solvate using gmx solvate -cp 
minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o 
system-solvated.gro.


WARNING: Masses and atomic (Van der Waals) radii will be guessed  based on 
residue and atom names, since they could not be definitively assigned from the 
information in your input
 files. These guessed numbers might deviate from the mass  and radius 
of the atom type. Please check the output  files if necessary.


could anybody tell me how to fix this? I run gmx solvate -h, but still have no 
idea.


Besides, I am confused about the difference between the martini22 ff and 
martini22p ff. when checking 5.0.4 manual, i found little information about 
martini. hope to receive guidance about this.


thanks in advance.
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[gmx-users] Martini CG water

[Ming Tang]

Dear all,


I am trying to learn simulation in gromacs 5.0.4 using martini force field, 
when learning the tutorial (http://md.chem.rug.nl/cgmartini/index.php/proteins) 
step by step, I got the following note when doing gmx slovate:

NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be removed 
in a future release when 'verlet' supports all interaction forms.


The CG water model ( water-box-CG_303K-1bar.gro) is downloaded from that 
tutorial website. I checked the 5.0.4 mannual, but found little information 
about Martini. could anybody tell me where to download the CG water model 
suitable for verlet? And what's the difference between Martini22 force field 
and Martini22p force field?

 Besides, when solvating the model using gmx solvate -cp 
minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o 
system-solvated.gro, I got the following warning:


WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

I run gmx solvate -h, but still have no idea to fix this problem. I have set 
Van der Walls distance in the command. could anybody give me some guidance?


Thanks in advance.
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Re: [gmx-users] first residue in chains warning issue

[Ming Tang]

Thanks. EM and NPT run without any warnings.

Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 5/12/15 8:10 AM, Ming Tang wrote:

 Thanks Justin,

 At first, I wanted to choose NONE in for both N and C terminus, but it gave 
 me the same warnings for both the first and the last residue in every chains. 
 However, choose NH3+/COO- and NH2/COOH just gave that warning for the first 
 residue.


Right, because choosing None is chemical nonsense in this context.

 The angles and bonds in .itp are like this:

 [ bonds ]
 ;  aiaj functc0c1c2c3
  1 2 2gb_2
  1 3 2gb_2
  1 4 2gb_21
  4 5 2gb_27

 [ angles ]
 ;  aiajak functc0c1c2
 c3
  2 1 3 2ga_10
  2 1 4 2ga_10
  2 1 5 2ga_11
  3 1 4 2ga_10
  3 1 5 2ga_11
  4 1 5 2ga_11
  1 5 6 2ga_13
  1 513 2ga_13
  6 513 2ga_13

 Just now, I tried to delete one H atom of the first residue in the input 
 .pdb, but got the same warnings for them. Is there  anything wrong with the 
 angle and bond?

Well, cross-reference what the atoms are and what the parameters should be.
That's your job, not mine :)  Energy minimization and a quick MD run will show
you if there are any problems; if things are missing or wrong (very unlikely,
but always check when you see warnings!) then the structure will be obviously
wrong very quickly.  Like I said, this is really most likely just some weird
case in the code that isn't handled elegantly, but there's not enough to go on
for a full debug.

-Justin

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
 Justin Lemkul
 Sent: Tuesday, 12 May 2015 9:35 PM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] first residue in chains warning issue



 On 5/11/15 6:48 PM, Ming Tang wrote:
 Hi Justin,

 Here is the output of pdb2gmx:

 Command line:
 pdb2gmx -f hyp_lys.pdb -o complex.gro -ignh -ter -ff gromos54a7
 -water SPC


 Using the Gromos54a7 force field in directory gromos54a7.ff

 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
 Reading hyp_lys.pdb...
 Read 20130 atoms
 Analyzing pdb file
 Splitting chemical chains based on TER records or chain id changing.
 There are 3 chains and 0 blocks of water and 3134 residues with 20130
 atoms

 chain  #res #atoms
 1 'A'  1054   6788
 2 'B'  1026   6554
 3 'C'  1054   6788

 All occupancies are one
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
 Atomtype 58
 Reading residue database... (gromos54a7) Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
 Using default: not generating all possible dihedrals Using default:
 excluding 3 bonded neighbors Using default: generating 1,4 H--H
 interactions Using default: removing proper dihedrals found on the
 same bond as a proper dihedral Residue 108 Sorting it all out...
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
 Opening force field file
 /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb

 Back Off! I just backed up topol.top to ./#topol.top.2# Processing
 chain 1 'A' (6788 atoms, 1054 residues) Analysing hydrogen-bonding
 network for automated assignment of histidine
protonation. 1365 donors and 1444 acceptors were found.
 There are 1748 hydrogen bonds
 Will use HISE for residue 105
 Will use HISE for residue 948
 Identified residue GLN1 as a starting terminus.
 Identified residue TYR1054 as a ending terminus.
 8 out of 8 lines of specbond.dat converted successfully Special Atom
 Distance matrix:
   MET2   MET19   MET55  MET102  HIS105  MET139  MET418
   SD15   SD136   SD369   SD678  NE2702   SD926  SD2692
  MET19   SD136   5.356
  MET55   SD369  16.259  10.913
 MET102   SD678  29.737  24.390  13.588
 HIS105  NE2702  30.104  24.755  13.935   0.427
 MET139   SD926  40.534  35.194  24.356  10.855  10.499
 MET418  SD2692 121.526 116.225 105.475  91.946  91.605  81.150
 MET567  SD3648 163.789 158.490 147.754 134.205 133.865 123.429  42.327
 MET838  SD5366 241.858 236.550 225.799 212.233 211.888 201.460 120.429
 HIS948 NE26069 273.040 267.735 256.991 243.424 243.081 232.655 151.608
 MET567  MET838
 SD3648  SD5366
 MET838  SD5366  78.135
 HIS948 NE26069 109.299  31.201
 Select start terminus type for GLN-1
0: NH3+
1: NH2
2: None
 1
 Start terminus GLN

Re: [gmx-users] HYL force field

[Ming Tang]

Dear Justin,

The protein contains 15 constituent HYL residue modified from LYS. I realized 
that I need to modify the .rtp, but have no idea about how to derive the 
parameters correctly. Do you have any suggestions for this?

thanks a lot.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul 
jalem...@vt.edu
Sent: Monday, 11 May 2015 9:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] HYL force field

On 5/10/15 10:12 PM, Ming Tang wrote:
 Hi, 范聪

 I have never worked with ligand, and will try to learn this tutorial.

I think you need to define what containing means - is it a constituent residue
of the protein sequence or is it a noncovalently bound ligand?  The approach in
both cases differs.  For the former, you need to create an .rtp entry and
process the chain with pdb2gmx.  For the latter, you need to generate a separate
topology for the bound ligand.

The proper method for parametrizing the ligand depends on the force field you
want to use.

-Justin

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ??
 Sent: Monday, 11 May 2015 11:03 AM
 To: gmx-us...@gromacs.org
 Cc: gromacs.org_gmx-users@maillist.sys.kth.se
 Subject: Re: [gmx-users] HYL force field

 Hello, can you treat HYL as ligand and build its forcefield parameters 
 referring to this  link 
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
 At 2015-05-11 08:39:39, Ming Tang m21.t...@qut.edu.au wrote:
 Dear all,

 I want to simulate a protein containing hydroxylysine (HYL). I checked all 
 the force fields, but no .rtp file includes the parameters of it. How can I 
 derive it correctly?

 Thanks.
 --
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--
==

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

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

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

==
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[gmx-users] first residue in chains warning issue

[Ming Tang]

Dear all,

I built a triple helix with 2 GLN and 1 SER being the first residue of the 
three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter 
-ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type 
for GLN-1  and SER-1, I came across the following warnings:

WARNING: WARNING: Residue 1 named GLN (SER) of a molecule in the input file was 
mapped to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the input file. 
Perhaps your atom and/or residue naming needs to be fixed.

Then, I checked the .pdb and .rtp files. The difference between GLN-1/SER-1 and 
GLN-n/SER-n (n1) is that GLN-1/SER-1 contains 2 more H atoms.

Residue GLN-1 in .pdb
ATOM  1  N   GLN A   1 -10.554  16.421  -0.030  1.00  0.00   N1+
ATOM  2  CA  GLN A   1 -10.080  16.667   1.238  1.00  0.00   C
ATOM  3  C   GLN A   1  -9.305  15.495   1.835  1.00  0.00   C
ATOM  4  O   GLN A   1  -9.636  14.335   1.608  1.00  0.00   O
ATOM  5  CB  GLN A   1 -11.222  17.053   2.210  1.00  0.00   C
ATOM  6  CD  GLN A   1 -11.943  17.895   4.480  1.00  0.00   C
ATOM  7  NE2 GLN A   1 -11.643  18.268   5.719  1.00  0.00   N
ATOM  8  OE1 GLN A   1 -13.093  17.905   4.041  1.00  0.00   O
ATOM  9  CG  GLN A   1 -10.784  17.445   3.612  1.00  0.00   C
ATOM 10  HE2 GLN A   1 -12.366  18.573   6.339  1.00  0.00   H
ATOM 11  HE2 GLN A   1 -10.694  18.243   6.032  1.00  0.00   H
ATOM 12  H   GLN A   1 -11.086  17.245  -0.422  1.00  0.00   H
ATOM 13  H   GLN A   1  -9.773  16.207  -0.708  1.00  0.00   H
ATOM 14  H   GLN A   1 -11.212  15.593  -0.048  1.00  0.00   H

Parameters in .rtp in gromos54a7
[ GLN ]
[ atoms ]
N N-0.31000 0
H H 0.31000 0
   CA   CH1 0.0 1
   CB   CH2 0.0 1
   CG   CH2 0.0 1
   CD C 0.29000 2
 OE1 O-0.45000 2
  NE2NT-0.72000 2
HE21 H 0.44000 2
HE22 H 0.44000 2
C C   0.450 3
O O  -0.450 3
[ angles ]
;  aiajak   gromos type
   -C N H ga_32
   -C NCA ga_31
H NCA ga_18
NCACB ga_13
NCA C ga_13
   CBCA C ga_13
   CACBCG ga_15
   CBCGCD ga_15
   CGCD   OE1 ga_30
   CGCD   NE2 ga_19
  OE1CD   NE2 ga_33
   CD   NE2  HE21 ga_23
   CD   NE2  HE22 ga_23
 HE21   NE2  HE22 ga_24
   CA C O ga_30
   CA C+N ga_19
O C+N ga_33

Further, I compared atoms of GLN in .pdb and .rtp, and changed 2 HE into HE21 
and HE22, but got the same warnings.

The simulation can be move forward to EM and NPT smoothly. Does this kind of 
warning affect the simulation results significantly?

Thanks in advance.

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Re: [gmx-users] HYL force field

[Ming Tang]

Hi, 范聪

I have never worked with ligand, and will try to learn this tutorial.
Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ??
Sent: Monday, 11 May 2015 11:03 AM
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] HYL force field

Hello, can you treat HYL as ligand and build its forcefield parameters 
referring to this  link 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
At 2015-05-11 08:39:39, Ming Tang m21.t...@qut.edu.au wrote:
Dear all,

I want to simulate a protein containing hydroxylysine (HYL). I checked all the 
force fields, but no .rtp file includes the parameters of it. How can I derive 
it correctly?

Thanks.
-- 
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[gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

[Ming Tang]

Hi，Justin

I have been told by an author of one journsl that pdb2gmx can convert PRO to 
HYP while generating. I did not find the option. Can you give me some advice.
Thanks
Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 4/30/15 6:46 AM, vidhya sankar wrote:
 Dear justin Thank you for you reply

 Also when i use g_enemat tool as follows


 g_enemat_d -f CNTPEPRSOLIONSfulllatest3.edr -groups group.dat -emat jnnff.xpm

 it shows the following error
 Opened CNTPEPRSOLIONSfulllatest3.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE1 
 (0,0)in energy file
 WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE2 (0,1)in 
 energy file
 group 1WARNING! could not find group (null):CYCLIPEPTIDE2-CYCLIPEPTIDE2 
 (1,1)in energy file

 Will select half-matrix of energies with 6 elements
 Last energy frame read 25000 time 5.000
 Will build energy half-matrix of 2 groups, 6 elements, over 25001 frames
 Segmentation fault (core dumped)
 though i set
 2
 CYCLIPEPTIDE1
 CYCLIPEPTIDE2as energy groups .my .mdp file whil running MD

 So why it shows error?


A seg fault is usually a bug.  There was a g_enemat seg fault in an old version,
but it was fixed.  If you're not using 5.0.4, you should be.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

[Ming Tang]

Thanks, Justin

It is a paper published in NANO-LETTERS!

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Friday, 1 May 2015 12:04 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?



On 4/30/15 9:57 AM, Mark Abraham wrote:
 Hi,

 Please do everyone the courtesy of starting a new email, rather than 
 replying to a digest and confusing the archive and email readers.

 On Thu, Apr 30, 2015 at 3:50 PM Ming Tang m21.t...@qut.edu.au wrote:

 Hi，Justin

 I have been told by an author of one journsl that pdb2gmx can convert 
 PRO to HYP while generating. I did not find the option. Can you give 
 me some advice.


 Get knowledgeable reviewers ;-) You can't do it with pdb2gmx. Some 
 building programs are suggested on the GROMACS website.


Perhaps one can play some tricks, but I agree with Mark.  Simply saying that 
pdb2gmx can do this is not true, at least not in a straightforward way.

The trick I might think of (caveat: untested!) is as follows:

1. Process the chain with normal PRO and build normal H on to the ring 2. Take 
that output and rename PRO-HYP, define .rtp and .hdb entries for HYP (or use 
whatever is already in the force field), rename the corresponding H atom to 
whatever the appropriate oxygen name is, and then re-process with pdb2gmx to 
build on the hydroxyl H atom 3. Minimize thoroughly

The above steps assume, of course, the use of an all-atom force field to get H 
built onto the ring.

This is a *very* crude approach and could distort geometry, so tread carefully. 
  The best approach is, as Mark says, use some molecule-editing software and 
build the structure appropriately.  My hack might work, but it's not the best 
way to do this.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] 회신: Re: Generating topology file containing HYP

[Ming Tang]

Hi, Sangeun

Thank you so much for your detailed instruction. I can mutate PRO to HYP now.
Regards,

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
sangeunjee
Sent: Friday, 1 May 2015 9:36 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] 회신: Re: Generating topology file containing HYP

Dear Ming Tang

I am also using free version. To concert proline to hydroxypropine, 1. Read 
your pdb file using discovery studio visualizer 2. You will find there is list 
of menu in the left side of the screen. There is an option to draw specific 
amino acids. Here you can choose mutate to change proline to other one. I hope 
it helps,

Sangeun Jee

div 원본 메시지 /divdiv발신: Ming Tang m21.t...@qut.edu.au 
/divdiv날짜:30/04/2015  02:09  (GMT-05:00) /divdiv수신: 
gmx-us...@gromacs.org /divdiv제목: Re: [gmx-users] Generating topology file 
containing HYP /divdiv /divDear, sangeun

Thanks for your help. I have downloaded and installed Discovery Studio 
Visualizer, and found only limited amount of its ability is available for free. 
Do you think I can convert proline into hydroxyproline using its free function?
Detail guidance will be appreciate.

Thanks in advance,
Best regards. 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of sang 
eun jee
Sent: Thursday, 30 April 2015 1:01 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Generating topology file containing HYP

Dear Ming Tang

As long as I know, Discovery studio visualizer can do the mutation from proline 
to hydroxyproline in a simple way.

Hope it helps,

Sangeun Jee

On Wed, Apr 29, 2015 at 5:42 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear all,

 I have a pdb file, and need to convert some of the proline to 
 hydroxyproline. Can I use pdb2gmx to convert proline to hydroxyproline 
 when generating the topology file?  If I cannot, then which kind of 
 software can be used to convert proline to hydroxyproline when 
 generating the topology file?

 Thanks in advance,
 Regards,
 Ming
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--
Post Doctoral Researcher
School of Materials Science and Engineering Georgia Institute of Technology
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Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

[Ming Tang]

Sorry, Mark

I was using a mobile on bed, and though it would be more convenience.
Anyway, I promise not doing this again.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Thursday, 30 April 2015 11:58 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

Hi,

Please do everyone the courtesy of starting a new email, rather than replying 
to a digest and confusing the archive and email readers.

On Thu, Apr 30, 2015 at 3:50 PM Ming Tang m21.t...@qut.edu.au wrote:

 Hi，Justin

 I have been told by an author of one journsl that pdb2gmx can convert 
 PRO to HYP while generating. I did not find the option. Can you give 
 me some advice.


Get knowledgeable reviewers ;-) You can't do it with pdb2gmx. Some building 
programs are suggested on the GROMACS website.

Mark


 Thanks
 Sent from my Huawei Mobile

 Justin Lemkul jalem...@vt.edu wrote:



 On 4/30/15 6:46 AM, vidhya sankar wrote:
  Dear justin Thank you for you reply
 
  Also when i use g_enemat tool as follows
 
 
  g_enemat_d -f CNTPEPRSOLIONSfulllatest3.edr -groups group.dat -emat
 jnnff.xpm
 
  it shows the following error
  Opened CNTPEPRSOLIONSfulllatest3.edr as single precision energy file 
  Will read groupnames from inputfile Read 2 groups group 0WARNING! 
  could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE1
 (0,0)in energy file
  WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE2 
  (0,1)in
 energy file
  group 1WARNING! could not find group 
  (null):CYCLIPEPTIDE2-CYCLIPEPTIDE2
 (1,1)in energy file
 
  Will select half-matrix of energies with 6 elements Last energy 
  frame read 25000 time 5.000 Will build energy half-matrix of 2 
  groups, 6 elements, over 25001 frames Segmentation fault (core 
  dumped) though i set
  2
  CYCLIPEPTIDE1
  CYCLIPEPTIDE2as energy groups .my .mdp file whil running MD
 
  So why it shows error?
 

 A seg fault is usually a bug.  There was a g_enemat seg fault in an 
 old version, but it was fixed.  If you're not using 5.0.4, you should 
 be.

 -Justin

 --
 ==

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

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

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

 ==
 --
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Re: [gmx-users] Generating topology file containing HYP

[Ming Tang]

Dear, sangeun

Thanks for your help. I have downloaded and installed Discovery Studio 
Visualizer, and found only limited amount of its ability is available for free. 
Do you think I can convert proline into hydroxyproline using its free function?
Detail guidance will be appreciate.

Thanks in advance,
Best regards. 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of sang 
eun jee
Sent: Thursday, 30 April 2015 1:01 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Generating topology file containing HYP

Dear Ming Tang

As long as I know, Discovery studio visualizer can do the mutation from proline 
to hydroxyproline in a simple way.

Hope it helps,

Sangeun Jee

On Wed, Apr 29, 2015 at 5:42 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear all,

 I have a pdb file, and need to convert some of the proline to 
 hydroxyproline. Can I use pdb2gmx to convert proline to hydroxyproline 
 when generating the topology file?  If I cannot, then which kind of 
 software can be used to convert proline to hydroxyproline when 
 generating the topology file?

 Thanks in advance,
 Regards,
 Ming
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[gmx-users] Generating topology file containing HYP

[Ming Tang]

Dear all,

I have a pdb file, and need to convert some of the proline to hydroxyproline. 
Can I use pdb2gmx to convert proline to hydroxyproline when generating the 
topology file?  If I cannot, then which kind of software can be used to convert 
proline to hydroxyproline when generating the topology file?

Thanks in advance,
Regards,
Ming
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Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories

[Ming Tang]

Hi，-e is end frame， -b is the start one.

Sent from my Huawei Mobile

Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote:

hi GMx user I simulated protein-ligand comolex with gromacs. total simulation 
time is 20ns. when I use trjconv for cutting the  trajectory  in  small   
subtrajectories from 1ps to 17000ps by following command:
trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000
I see following text in terminal window;
Reading frame   0 time 1.000
Precision of md-nopbc.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
 -  frame   3500 time 17000.000-  frame   3000 time 16000.000
I think the generated trajectory is incomplete because saved frame is 
incomplete. please guide me.
Many thanks tobest
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Re: [gmx-users] Pull code

[Ming Tang]

Try constraint method. It works .

Sent from my Huawei Mobile

Alex nedoma...@gmail.com wrote:

That is not an option for me, all groups must exhibit full dynamics, so
partial restraint seems like a decent option.
It is my understanding that explicitly moving only one group is impossible
in the new version. Is that the case?

Thanks,

Alex


On Wed, Apr 22, 2015 at 5:58 PM, Ming Tang m21.t...@qut.edu.au wrote:

 Hi, Alex

 I tried this code plus freeze all of the atoms in the group needed to stay
 in place, and it worked well.
 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex
 Sent: Thursday, 23 April 2015 9:47 AM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] Pull code

 The CNT group is actually very strongly restrained, not the entire atomic
 population, but the edges. So, from inspecting my code, everything looks
 right?

 Thanks,

 Alex



  Not really.  The constraint option keeps a rigid constraint between
  the
  two groups.  The umbrella keyword specifies a harmonic potential,
  whose strength is tunable.  Otherwise, the two methods are identical.
 
  If one group needs to stay in place, it needs position restraints
  applied
  to it.  If the desired separation is not occurring, either a larger
  spring force constant or a faster pull rate is needed.
  
  -Justin
 
 
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Re: [gmx-users] g_wham error in umbrella simulation

[Ming Tang]

Hi, Justin

You are right. Finally, I got both of the curves. Happy! 
Thanks for your guidance.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Wednesday, 22 April 2015 10:18 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_wham error in umbrella simulation



On 4/22/15 4:46 AM, Ming Tang wrote:
 Hi, Justin

 Thanks a lot. Dos2unix works. There is even no blank space in every 
 line. The problem is that I downloaded those .dat files from the 
 internet, which were created in windows system. But I got another 
 problem. Following your umbrella sampling tutorial, I got the PMF 
 curve. The trend of the curve is quite close to that of the curve in 
 the tutorial. But, the ΔG is -31, 20 more compared to
 -50.5 in the tutorial. Besides, I only get one histogram, the data of 
 the

You won't get the value in the tutorial unless you follow the published 
protocol.  The tutorial is an abbreviated version of a more complex protocol 
involving (1) prior simulation of 100 ns and (2) asymmetrical window 
distribution.  I believe this should be stated already in the tutorial.

 rest histograms are zero (one horizontal line). Do you have any 
 suggestions for me about what's wrong with my simulation?

You're probably just not plotting the histogram file right.

xmgrace -nxy histo.xvg

to show all the histograms.

-Justin

--
==

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

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

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

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[gmx-users] Problems in the modelling of interaction between peptide and copper

[Ming Tang]

Dear all,

I got a problem when modelling the interaction of a peptide and copper. I am 
using the force field of opls-aa. The charge of copper atoms are defined as 
zero and the non-bonded parameters are obtained from the CU ions, which can be 
found in opls-aa.

I applied smd and found that the peptide is approaching the copper surface and 
stopped when it is very close to the surface, due to some abnormal interaction. 
The whole process seems quite reasonable, however, when I rerun the simulation 
to obtain the interaction energy, for the vdw interaction between peptide and 
copper is zero, absolute zero, in the whole process.

Can anyone give me some suggestions? Is my model reasonable? I am not so 
confident with modelling strategy of using the LJ parameters for copper bulk 
material. Also the zero interaction energy is another big issue.

Cheers,
Tng
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Re: [gmx-users] Pull code

[Ming Tang]

Hi， Justin
I will try whether i can set reference group using umbrella later.

Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 4/22/15 7:17 PM, Ming Tang wrote:
 Hi，Alex

 You can try constraint. In umbrella， both 2 groups move.


Not really.  The constraint option keeps a rigid constraint between the two
groups.  The umbrella keyword specifies a harmonic potential, whose strength
is tunable.  Otherwise, the two methods are identical.

If one group needs to stay in place, it needs position restraints applied to it.
  If the desired separation is not occurring, either a larger spring force
constant or a faster pull rate is needed.

-Justin

 Sent from my Huawei Mobile

 Alex nedoma...@gmail.com wrote:

 Hi all,

 I have a group (DNA) I'd like to translate relative to the other group
 (CNT) along the Z-direction so that DNA is the only group that's actually
 moving.

 The code I had prior to what I have now worked under GMX 4.5.something.
 Since the syntax has changed in 5.0.x, I found Justin's old suggestions,
 and this is what I have now:

 ;Pull code

 pull= umbrella

 pull_geometry   = direction

 pull_coord1_vec = 0.0 0.0 1.0

 pull_start  = yes

 pull_coord1_init= 0.0

 pull_ngroups= 2

 pull_ncoords= 1

 pull_coord1_groups  = 1 2

 pull_group1_name= CNT

 pull_group2_name= DNA

 pull_coord1_rate1   = 0.0002  ;nm per ps

 pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2

 ;end pull code


 Does this look right? My simulation isn't nearly done, but I am looking at
 the Z-displacement in pullx.xvg and it just oscillates around a single
 value. The simulated time is now about 1.5 ns.


 Thank you,


 Alex
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--
==

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

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

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

==
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Re: [gmx-users] Pull code

[Ming Tang]

Hi, Justin

I am confusing about what is the difference between the rigid constraint in 
constraint pull method and the harmonic potential using umbrella.
The force acts directly on the centre of mass of the group in constraint, and 
the force acts on the center of mass of the group through a spring when using 
umbrella pull method.
Am I right?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 23 April 2015 9:22 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pull code



On 4/22/15 7:17 PM, Ming Tang wrote:
 Hi，Alex

 You can try constraint. In umbrella， both 2 groups move.


Not really.  The constraint option keeps a rigid constraint between the two 
groups.  The umbrella keyword specifies a harmonic potential, whose strength 
is tunable.  Otherwise, the two methods are identical.

If one group needs to stay in place, it needs position restraints applied to 
it. 
  If the desired separation is not occurring, either a larger spring force 
constant or a faster pull rate is needed.

-Justin

 Sent from my Huawei Mobile

 Alex nedoma...@gmail.com wrote:

 Hi all,

 I have a group (DNA) I'd like to translate relative to the other group
 (CNT) along the Z-direction so that DNA is the only group that's 
 actually moving.

 The code I had prior to what I have now worked under GMX 4.5.something.
 Since the syntax has changed in 5.0.x, I found Justin's old 
 suggestions, and this is what I have now:

 ;Pull code

 pull= umbrella

 pull_geometry   = direction

 pull_coord1_vec = 0.0 0.0 1.0

 pull_start  = yes

 pull_coord1_init= 0.0

 pull_ngroups= 2

 pull_ncoords= 1

 pull_coord1_groups  = 1 2

 pull_group1_name= CNT

 pull_group2_name= DNA

 pull_coord1_rate1   = 0.0002  ;nm per ps

 pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2

 ;end pull code


 Does this look right? My simulation isn't nearly done, but I am 
 looking at the Z-displacement in pullx.xvg and it just oscillates 
 around a single value. The simulated time is now about 1.5 ns.


 Thank you,


 Alex
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--
==

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

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

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

==
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Re: [gmx-users] Pull code

[Ming Tang]

Hi, Alex

I tried this code plus freeze all of the atoms in the group needed to stay in 
place, and it worked well.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex
Sent: Thursday, 23 April 2015 9:47 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pull code

The CNT group is actually very strongly restrained, not the entire atomic 
population, but the edges. So, from inspecting my code, everything looks right?

Thanks,

Alex



 Not really.  The constraint option keeps a rigid constraint between 
 the
 two groups.  The umbrella keyword specifies a harmonic potential, 
 whose strength is tunable.  Otherwise, the two methods are identical.

 If one group needs to stay in place, it needs position restraints 
 applied
 to it.  If the desired separation is not occurring, either a larger 
 spring force constant or a faster pull rate is needed.
 
 -Justin


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Re: [gmx-users] Pull code

[Ming Tang]

Hi，Alex

You can try constraint. In umbrella， both 2 groups move.

Sent from my Huawei Mobile

Alex nedoma...@gmail.com wrote:

Hi all,

I have a group (DNA) I'd like to translate relative to the other group
(CNT) along the Z-direction so that DNA is the only group that's actually
moving.

The code I had prior to what I have now worked under GMX 4.5.something.
Since the syntax has changed in 5.0.x, I found Justin's old suggestions,
and this is what I have now:

;Pull code

pull= umbrella

pull_geometry   = direction

pull_coord1_vec = 0.0 0.0 1.0

pull_start  = yes

pull_coord1_init= 0.0

pull_ngroups= 2

pull_ncoords= 1

pull_coord1_groups  = 1 2

pull_group1_name= CNT

pull_group2_name= DNA

pull_coord1_rate1   = 0.0002  ;nm per ps

pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2

;end pull code


Does this look right? My simulation isn't nearly done, but I am looking at
the Z-displacement in pullx.xvg and it just oscillates around a single
value. The simulated time is now about 1.5 ns.


Thank you,


Alex
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Re: [gmx-users] g_wham error in umbrella simulation

[Ming Tang]

Hi, Justin

Thanks a lot.
Dos2unix works. There is even no blank space in every line. The problem is that 
I downloaded those .dat files from the internet, which were created in windows 
system. But I got another problem. 
Following your umbrella sampling tutorial, I got the PMF curve. The trend of 
the curve is quite close to that of the curve in the tutorial. But, the ΔG is 
-31, 20 more compared to -50.5 in the tutorial. Besides, I only get one 
histogram, the data of the rest histograms are zero (one horizontal line). Do 
you have any suggestions for me about what's wrong with my simulation?
Thank you.


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 20 April 2015 10:17 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_wham error in umbrella simulation



On 4/19/15 9:53 PM, Ming Tang wrote:
 Dear all,

 I am doing an umbrella simulation, and come across the following error.

 Command line:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 
 2000

 Found 27 tpr and 27 pull force files in tpr-files.dat and 
 pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic 
 determination of boundaries...

 ---
 Program g_wham, VERSION 5.0.4
 Source code file: 
 /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767

 Fatal error:
 . Should be tpr, xvg, or pdo.0.tpr


Is this a copy/paste problem or is this really what the line said?  The error 
message should be Unknown file of type (something). Should be tpr, xvg, or 
pdo.  Note the 0.tpr that is tacked on to the end and the lack of preceding 
text.  Any weird line endings in your tpr-files.dat file?  Check and run 
dos2unix if needed.  The presence of 0.tpr somewhat suggests the very first 
line is causing a problem, even though it appears gmx wham understands how many 
files it should find; it just can't determine the right file names/types.

-Justin

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

 tpr-files.dat:
 umbrella0.tpr
 umbrella137.tpr
 umbrella155.tpr
 umbrella163.tpr
 umbrella169.tpr
 umbrella174.tpr
 umbrella179.tpr
 umbrella185.tpr
 umbrella199.tpr
 umbrella206.tpr
 umbrella223.tpr
 umbrella239.tpr
 umbrella257.tpr
 umbrella275.tpr
 umbrella291.tpr
 umbrella308.tpr
 umbrella324.tpr
 umbrella344.tpr
 umbrella369.tpr
 umbrella383.tpr
 umbrella392.tpr
 umbrella422.tpr
 umbrella450.tpr
 umbrella463.tpr
 umbrella479.tpr
 umbrella497.tpr
 umbrella499.tpr

 pullf-files.dat
 pullf0.xvg
 pullf137.xvg
 pullf155.xvg
 pullf163.xvg
 pullf169.xvg
 pullf174.xvg
 pullf179.xvg
 pullf185.xvg
 pullf199.xvg
 pullf206.xvg
 pullf223.xvg
 pullf239.xvg
 pullf257.xvg
 pullf275.xvg
 pullf291.xvg
 pullf308.xvg
 pullf324.xvg
 pullf344.xvg
 pullf369.xvg
 pullf383.xvg
 pullf392.xvg
 pullf422.xvg
 pullf450.xvg
 pullf463.xvg
 pullf479.xvg
 pullf497.xvg
 pullf499.xvg

 I used this method several times before, and did not come across this 
 problem. could anybody tell me where is the problem?
 Thanks


--
==

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

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

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

==
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Re: [gmx-users] g_wham error in umbrella simulation

[Ming Tang]

Thanks for your advice.
I just checked. There is no empty line at the end of the .dat files.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
Kortzak, Daniel
Sent: Monday, 20 April 2015 8:01 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] g_wham error in umbrella simulation

Maybe some empty lines at the end of your .dat files.

Dear all,

I am doing an umbrella simulation, and come across the following error.

Command line:
  g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000

Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, 
respectively Reading 13 tpr and pullf files Automatic determination of 
boundaries...

---
Program g_wham, VERSION 5.0.4
Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, 
line: 1767

Fatal error:
. Should be tpr, xvg, or pdo.0.tpr

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

tpr-files.dat:
umbrella0.tpr
umbrella137.tpr
umbrella155.tpr
umbrella163.tpr
umbrella169.tpr
umbrella174.tpr
umbrella179.tpr
umbrella185.tpr
umbrella199.tpr
umbrella206.tpr
umbrella223.tpr
umbrella239.tpr
umbrella257.tpr
umbrella275.tpr
umbrella291.tpr
umbrella308.tpr
umbrella324.tpr
umbrella344.tpr
umbrella369.tpr
umbrella383.tpr
umbrella392.tpr
umbrella422.tpr
umbrella450.tpr
umbrella463.tpr
umbrella479.tpr
umbrella497.tpr
umbrella499.tpr

pullf-files.dat
pullf0.xvg
pullf137.xvg
pullf155.xvg
pullf163.xvg
pullf169.xvg
pullf174.xvg
pullf179.xvg
pullf185.xvg
pullf199.xvg
pullf206.xvg
pullf223.xvg
pullf239.xvg
pullf257.xvg
pullf275.xvg
pullf291.xvg
pullf308.xvg
pullf324.xvg
pullf344.xvg
pullf369.xvg
pullf383.xvg
pullf392.xvg
pullf422.xvg
pullf450.xvg
pullf463.xvg
pullf479.xvg
pullf497.xvg
pullf499.xvg

I used this method several times before, and did not come across this problem. 
could anybody tell me where is the problem?
Thanks









Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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[gmx-users] g_wham error in umbrella simulation

[Ming Tang]

Dear all,

I am doing an umbrella simulation, and come across the following error.

Command line:
  g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000

Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, 
respectively
Reading 13 tpr and pullf files
Automatic determination of boundaries...

---
Program g_wham, VERSION 5.0.4
Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, 
line: 1767

Fatal error:
. Should be tpr, xvg, or pdo.0.tpr

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

tpr-files.dat:
umbrella0.tpr
umbrella137.tpr
umbrella155.tpr
umbrella163.tpr
umbrella169.tpr
umbrella174.tpr
umbrella179.tpr
umbrella185.tpr
umbrella199.tpr
umbrella206.tpr
umbrella223.tpr
umbrella239.tpr
umbrella257.tpr
umbrella275.tpr
umbrella291.tpr
umbrella308.tpr
umbrella324.tpr
umbrella344.tpr
umbrella369.tpr
umbrella383.tpr
umbrella392.tpr
umbrella422.tpr
umbrella450.tpr
umbrella463.tpr
umbrella479.tpr
umbrella497.tpr
umbrella499.tpr

pullf-files.dat
pullf0.xvg
pullf137.xvg
pullf155.xvg
pullf163.xvg
pullf169.xvg
pullf174.xvg
pullf179.xvg
pullf185.xvg
pullf199.xvg
pullf206.xvg
pullf223.xvg
pullf239.xvg
pullf257.xvg
pullf275.xvg
pullf291.xvg
pullf308.xvg
pullf324.xvg
pullf344.xvg
pullf369.xvg
pullf383.xvg
pullf392.xvg
pullf422.xvg
pullf450.xvg
pullf463.xvg
pullf479.xvg
pullf497.xvg
pullf499.xvg

I used this method several times before, and did not come across this problem. 
could anybody tell me where is the problem?
Thanks

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Re: [gmx-users] force field problem....

[Ming Tang]

Hi, Justin
Thank you so much. I should be much more cautious in the future.
there is another interesting thing. why doesn't it give the warning regarding 
mismatching between CLA and CL when I use MG in the pdb and topol file?
I did not copy CN88. actually, I typed it. I got those 2 parameters from 
oplsaa. I found that in ffnanonbonded.itp in charmm27.ff, MG and CAL in 
different types of pairs has the same sigma1-4 and epsilon 1-4, so I give SR 
the same as well.

Sent from my Huawei Mobile

Justin Lemkul jalem...@vt.edu wrote:



On 4/16/15 7:12 AM, Kamalesh Roy wrote:
 Dear all,

 please suggest for the topology for oleic acid..
 The information retreived after we run editconf...

 as a result atoms of the molecule becoming non bonded..in the box..


editconf doesn't add or remove bonds.  What you see in VMD (or whatever) is not
necessarily true (only the topology is definitive), but if the geometry is bad
then you'll get weird-looking states.  Your input coordinates could be messed up
somehow.

 8 out of 8 lines of specbond.dat converted successfully
 Checking for duplicate atoms
 Generating any missing hydrogen atoms and/or adding termini.
 Now there are 1 residues with 20 atoms
 Making bonds...
 No bonds
 Generating angles, dihedrals and pairs...
 Making cmap torsions...There are0 dihedrals,0 impropers,0 angles
   0 pairs,0 bonds and 0 virtual sites

Your .rtp entry is faulty if this is the outcome.

-Justin

 Total mass 279.445 a.m.u.
 Total charge -1.000 e
 Writing topology

 Back Off! I just backed up oleic1.itp to ./#oleic1.itp.1#


--
==

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

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

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

==
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