AMBER Archive (2004)

Subject: RE: AMBER: Sander : Vrand flag

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Mon Aug 23 2004 - 14:54:52 CDT

Dear Dr. Ross,
 Thank you for all the informatiom you are providing, that too in real quick time.
We really appreciate that.
 One last question is, is it possible to control the density of the system, so that after adding water molecules, I can make the density unifom ( density of water is 1)
 I am using Amber7.
 
 
Thank you again,
 
Regards,
Sachin Patil,
============
Graduate student,
Dept. of Medicinal & Biological Chemistry
College of Pharmacy
University of Toledo,
Toledo, Ohio 43606

 

Ross Walker <ross_at_rosswalker.co.uk> wrote:
Dear Sachin,
 
A couple of things to try. It is possible, although I am not sure, that the extra water molecules you are adding are not subject to the constraint force of the solvent cap and so can boil off into space. Adding these extra waters is also likely to greatly increase the density at the regions in which they are being added leading to large initial forces. If you think about it you have a droplet of water at a reasonable density to which you are adding extra waters. Hence the effective "pressure" inside the droplet is increasing significantly. I would try adding your extra waters BEFORE you add the solvent cap. In this way you won't increase the density since the solvatecap command will add less waters to compensate.
 
The reason the temperature is going up so high is that your system is exploding. The first sign of an "exploding" system is when the temperature rapidly shoots up. The temperature coupling is only weak so doesn't have time to 'correct' for this sudden increase in kinetic energy.
 
As for the vrand setting I would leave this at zero since it will greatly effect the dynamics of your system and mask what you are trying to measure. I would avoid ntt=2 for the moment and try and see if you get stable dynamics using a simple Berendsen thermostat. Set ntt=1 and tautp to something reasonably small like 1.0ps. Then I would take you solvent cap system and minimise if for quite a bit (Ca 5000 steps) before you move to any MD. Then try setting tempi=0 and temp0=300 and let your system slowly heat up. You could run say 20ps of MD here and dump the coordinates every step. In this way you will be able to visualise the fine dynamics of your system and if it blows up you will be able to see from where this happens and hopefully have a better chance of fixing it.
 
I would also try increasing the force constant of the water cap (FCAP) above the default (which I think is 1). Note you may also need to manually turn on the water cap in Amber 7. In amber 8 it is turned on by default if cap information is detected in the prmtop file. This may not be true for Amber 7 - I would check your output carefully.
 
All the best
Ross
 

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

 
 

---------------------------------
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of sachin patil
Sent: 23 August 2004 12:08
To: amber_at_scripps.edu
Subject: RE: AMBER: Sander : Vrand flag

Dear Dr. Ross Walker,
 I am trying to visualize movement of water molecules and their involment in the ligand binding. I have a receptor and ligand system which is around 6500 atoms big. I solvated it with a watercap and then manually added few water molecules in the system.
 When I load this modified pdb file in Xleap and make a "check" it gives me couple of error messages one of which is for water molecules.
I have restrained a few hydrogen bonds and the receptor to it position ( force constant 2). I am running nonperiodic conditions.I had set the temperature to be 298 K, but during the course of simulation the temperatures go above 350 K and the water molecules boil.
 
 (Interestingly, with another system which has no manually added water molecules the simulation goes fine. Eventhough the temperatures and high, similar to above.)
 
Since I just wanted the surface of interst, i.e. ligand binding site to be solvated so I added a water cap. If I solvate the entire system (so as to run periodic bounadry condition the system will be huge.)
 And since I wanted to control the temperatures, I set vrand=1 ( since i couldnot use Longevian alorithm ntt=3, with amber7.) and it took the simulation through.
 Do you still suggest me to solvate the entire system and then run periodic boundary
coinditions after manually adding water molecules?
 
 Or shall I check the system for any close contacts.
 In that case can you please brief me how the detalied initial minimization should be.As if now, I first minimize the water molecules and then the entire system.
 I have attached the input and sample output files below.
 
Thank You
 
Regards,
Sachin Patil,
============
Graduate student,
Dept. of Medicinal & Biological Chemistry
College of Pharmacy
University of Toledo,
Toledo, Ohio 43606
 
Follwing is the sample out put-
 
 =======================================================
 
Setting new random velocities at step 8500
 NSTEP = 8500 TIME(PS) = 218.500 TEMP(K) = 149.65 PRESS = 0.0 Etot = -17275.3978 EKtot = 3503.8761 EPtot = -20779.2738 BOND = 1126.2674 ANGLE = 3085.7870 DIHED = 3889.4866 1-4 NB = 1416.2147 1-4 EEL = 13519.4021 VDWAALS= -1183.8538 EELEC = -43371.0430 EHBOND = 0.0000 RESTRAINT = 738.4651 EAMBER (non-restraint) = -21517.7389
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
 NSTEP = 8550 TIME(PS) = 218.550 TEMP(K) = 300.98 PRESS = 0.0 Etot = -11965.3497 EKtot = 7046.9539 EPtot = -19012.3036 BOND = 1099.3445 ANGLE = 3024.5770 DIHED = 3922.5966 1-4 NB = 1448.0821 1-4 EEL = 13583.3557 VDWAALS= -1153.0540 EELEC = -41662.9215 EHBOND = 0.0000 RESTRAINT = 725.7160 EAMBER (non-restraint) = -19738.0196
-------------------------------------------------------------------------- -------------------------------------------------------------------------
 
 Here is the input file:
 
 &cntrl nstlim=190000,dt=0.001,
cut=12,ntb=0,nscm=1000, temp0=298,
tempi=298, vrand=100,ntt=1,
irest=1,ntx=5,nmropt=1, ntr=1,tautp=2.0,
fcap=.5, ntf=2, ntc=2,
ivcap=1,ntwe=500, ntwx=500, ntpr=50,
ntwr=5000, nrespa=1,matcap=6178, &end
&wt type='END'
&end
DISANG=./distfinal.rst
LISTOUT=POUT
group input for restrained atoms
2.0
RES 1 375
END
END

Ross Walker <ross_at_rosswalker.co.uk> wrote:
Dear Sachin
 
By setting vrand=100 you are randomising the velocities every 100 steps. This is probably not a good idea for the problem you are trying to solve. The fact that your system is exploding suggests that something is wrong with it. How did you create it? You probably have some very close contacts somewhere.
 
You also appear to be running a vacuum simulation but you talk about waters? How did you solvate your system? Did you add a solvent cap and a restraint force on the cap? If not then your system is likely to just boil off into space. Ideally if you want to run a solvated system you should use periodic boundaries.
 
I would try running extensive minimisation of your system first. Then try heating it slowly (possibly with a time step as short as 0.5fs if you have to) from 0 to 100K or so over 20ps at constant volume, assuming you can run periodic boundaries. If it is stable here then try slowly increasing the temperature over another 20ps or so to 300K. Then equilibrate for a while at 300K before switching to constant pressure.
 
If you still have problems please post details about your system as well as the input and output files.
 
All the best
Ross
 

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

---------------------------------
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of sachin patil
Sent: 23 August 2004 11:00
To: amber_at_scripps.edu
Subject: AMBER: Sander : Vrand flag

Dear Amber Users,
In the MD simulations I am curently running, the system was constanly exploding and I could see few water molecules out of the systems. And was getting an error in the MDOUT file as-
The system has extended beyond the extent of the virtual box..................
.....restarting shold resolve the error.
And the tempratures were constantly getiing higher and higher.
 
But when I set vrand=100 the simulation went throught just fine. But now my problem is, the temperature of the system is too cold after every 100 steps.
 
I dont know the implications of this on my system.And I am not sure what effect this has on the final results.
So any experiences on similar problems, answers, suggestions or comments are wel-comed.
 
Thank You,
 
Sachin Patil,
============
Graduate student,
Dept. of Medicinal & Biological Chemistry
College of Pharmacy
University of Toledo,
Toledo, Ohio 43606
 
Follwing is the sample out put-
 
 =======================================================
 
Setting new random velocities at step 8500
 NSTEP = 8500 TIME(PS) = 218.500 TEMP(K) = 149.65 PRESS = 0.0 Etot = -17275.3978 EKtot = 3503.8761 EPtot = -20779.2738 BOND = 1126.2674 ANGLE = 3085.7870 DIHED = 3889.4866 1-4 NB = 1416.2147 1-4 EEL = 13519.4021 VDWAALS= -1183.8538 EELEC = -43371.0430 EHBOND = 0.0000 RESTRAINT = 738.4651 EAMBER (non-restraint) = -21517.7389
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
 NSTEP = 8550 TIME(PS) = 218.550 TEMP(K) = 300.98 PRESS = 0.0 Etot = -11965.3497 EKtot = 7046.9539 EPtot = -19012.3036 BOND = 1099.3445 ANGLE = 3024.5770 DIHED = 3922.5966 1-4 NB = 1448.0821 1-4 EEL = 13583.3557 VDWAALS= -1153.0540 EELEC = -41662.9215 EHBOND = 0.0000 RESTRAINT = 725.7160 EAMBER (non-restraint) = -19738.0196
-------------------------------------------------------------------------- -------------------------------------------------------------------------
 
 Here is the input file:
 
 &cntrl nstlim=190000,dt=0.001,
cut=12,ntb=0,nscm=1000, temp0=298,
tempi=298, vrand=100,ntt=1,
irest=1,ntx=5,nmropt=1, ntr=1,tautp=2.0,
fcap=.5, ntf=2, ntc=2,
ivcap=1,ntwe=500, ntwx=500, ntpr=50,
ntwr=5000, nrespa=1,matcap=6178, &end
&wt type='END'
&end
DISANG=./distfinal.rst
LISTOUT=POUT
group input for restrained atoms
2.0
RES 1 375
END
END

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