Re: [gmx-users] Potential Energy

Abraham wrote: > > > - Original Message - > From: Yanmei Song > Date: Wednesday, January 27, 2010 10:58 > Subject: Re: [gmx-users] Potential Energy > To: jalem...@vt.edu, Discussion list for GROMACS users < > gmx-users@gromacs.org> > > > Dear Justin

Re: [gmx-users] Potential Energy

b.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > P

[gmx-users] Potential Energy

potential energy is usually a big negative number? Does this mean that my force field parameter or molecule structure have problems? Thanks in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] OPLS force field

great thankful. -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&#

Re: [gmx-users] Why density increase with increasing the cutoff length?

n der Spoel wrote: > On 12/21/09 8:03 AM, Yanmei Song wrote: > >> Dear Users: >> >> Anyone can explain why the density of the water models increase with >> increase the cutoff length. I tried a couple water models in >> reaction-field, PME simulations.The cutoff l

[gmx-users] Why density increase with increasing the cutoff length?

why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

: invalid fit: e.e. 15.6513 a 2.17585 tau1 28.9321 tau2 46.3966 Will use a single exponential fit for set 1 Set 1: err.est. 21.0339 a 1 tau1 15.1648 tau2 0 I really appreciate your patience and help! On Fri, Nov 20, 2009 at 3:07 PM, Justin A. Lemkul wrote: > > > Yanmei So

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

. I thought the error should be calculated as 1/29.5=0.034. Thank you again for your help! On Fri, Nov 20, 2009 at 12:35 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Users: >> >> Anyone knows how to get the standard errors of the results based

[gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

[gmx-users] bonds that rotated more than 30 degrees:

: Anyone knows what is the problem and how i can fix it? Thanks -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] MD fatal error :wrong string length 0 for string buf

what version is the tpr file? The one corresponding to mdrun 3.3.3? What do you mean? I used gromacs-3.3.3 before and now. the same system and I did not have the problem before. On Thu, Oct 29, 2009 at 2:06 PM, David van der Spoel wrote: > Yanmei Song wrote: > >> Dear All:

[gmx-users] MD fatal error :wrong string length 0 for string buf

. Any suggestions would be greatly appreciated Thanks -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] How to get the rotational correlation time of the non-equilibrium simulation

your help in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Dear Justin: Thank you so much for your answer. That helps a lot! On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Thanks for your response. >> >> The reason I am doing this is that I wanted to

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Users: >> >> I was running a system by non-equilibrium MD using a plain Cut-off for the >> electrostatics: >> >> title = water >> cpp = /lib/cpp >> c

[gmx-users] The Cut-off for coulombtype heat up the water system?

in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Viscosity using periodic perturbation method

I read some literature on periodic perturbation > method. they all used NVT. I did not found any information about this on > the manual. Can I use NPT Non-equilibrium MD in order to use periodic > perturbation method? Thanks in advance! > -- > Yanmei Song > Ph.D. Candidate > De

Re: [gmx-users] Viscosity using periodic perturbation method

s method require NVT ensemble simulation in > stead of NPT ? Because I read some literature on periodic perturbation > method. they all used NVT. I did not found any information about this on > the manual. Can I use NPT Non-equilibrium MD in order to use periodic > perturbation method?

[gmx-users] Viscosity using periodic perturbation method

this on the manual. Can I use NPT Non-equilibrium MD in order to use periodic perturbation method? Thanks in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users

Re: [gmx-users] shift function for vdwtype and density

ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 On Tue, May 19, 2009 at 11:12 AM, Yanmei Song wrote: > Dear Da

Re: [gmx-users] shift function for vdwtype and density

> Justin A. Lemkul wrote: > >> >> >> Yanmei Song wrote: >> >>> Dear Justin: >>> >>> Yes and I tried dispersion correction and it gives a larger density than >>> I expected. The density of the polymer by vdwtype=shift is more close

Re: [gmx-users] shift function for vdwtype and density

= 0, rvdw = > 1.2) > Density: 962 kg/m^3 > > Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2) > Density: 983 kg/m^3 > > -Justin > > > Justin A. Lemkul wrote: > >> >> >> Yanmei Song wrote: >> >>> Dear Justin:

Re: [gmx-users] shift function for vdwtype and density

density? Thank you so much! On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Yes. Before I do the water+polymer, I did both the bulk systems >> separately. The density of TIP5P I mentioned earlier is the r

Re: [gmx-users] shift function for vdwtype and density

did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >

Re: [gmx-users] shift function for vdwtype and density

. Thanks! On Mon, May 18, 2009 at 3:33 PM, Mark Abraham wrote: > Yanmei Song wrote: > >> Dear All: >> >> I found when I changed the vdwtype from cut-off to shift, the density of >> the system decrease significantly.All the other setting in the mdp file >> remai

[gmx-users] shift function for vdwtype and density

Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? -- Yanmei Song Ph.D

Re: [gmx-users] Re: parameter of RB potential for OPLS force field

per to see if the > parameters will suit your needs. > > If you need an R-B dihedral, you may have to parameterize it yourself; not > an easy task. > > -Justin > > Yanmei Song wrote: > >> They are CH3-SI-O-SI, SI-O-SI-CH3 and SI-O-SI-O. I have looked up >> ffoplsaab

[gmx-users] Re: parameter of RB potential for OPLS force field

wrote: > > > Yanmei Song wrote: > >> Yes, I have read that part and still have no idea how can I do that. That >> part tells us how to transfer from the OPLS parameters Vi to RB potential in >> GROMOS force field Ci. Now what I have is phi and k for periodic potentia

[gmx-users] Re: parameter of RB potential for OPLS force field

individuals who may be able to > help you. > > That said, read the manual, section 4.2.12. > > -Justin > > > Yanmei Song wrote: > >> Dear Justin: >> >> If I have the parameters of GROMOS force field for the proper dihedral, >> which i think they are

[gmx-users] parameter of RB potential for OPLS force field

I can transfer this parameter to RB parameters? Or these two potentials have no connections? Thanks -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Pressure coupling and cut-off

parameters are fixed, the density is independent of the MD procedure? I am using NPT ensemble with the mdp I mentioned before with added vdwtype = shift. On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Tha

Re: [gmx-users] Pressure coupling and cut-off

off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear All: >> >> I have question about the pressure coupling. I have done a

[gmx-users] Pressure coupling and cut-off

er the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineeri

Re: [gmx-users] Some molecules disconnected into many parts after EM

something wrong with the 4.0.4. How can I fix this? Anyone had the same problem before? On Fri, May 8, 2009 at 1:04 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Sorry to bother so many times. After EM everything looks fine. However th

Re: [gmx-users] Some molecules disconnected into many parts after EM

ed in classical MD so there > is likely nothing to be concerned about. > > -Justin > > Yanmei Song wrote: > >> Dear Justin: >> >> Thanks for your message. >> >> When I open the gro file using VMD it shows: >> >> atom:1950 >> bonds 1907

Re: [gmx-users] Some molecules disconnected into many parts after EM

chains in the box. This morning I found that it seems the problem was resolved by increasing the box size. Why is that? On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear users: >> >> I set up a 8nm cubic box with 6 long chain

[gmx-users] Some molecules disconnected into many parts after EM

how to solve the problem? Thanks in advance! -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/sea

[gmx-users] How to set up the cut-off radius

or systems and i want to be consistent. #2: How large should the cut-off be? Do I have to set up the cut-off to be larger than the dimension of the single molecule? Thank you so much for your help in advance!* -- Yanmei Song Department of Chemical Engin

Re: [gmx-users] Energy minimization error by GMX 4.0.4

Thank you so much for all the helpful response. On Wed, May 6, 2009 at 4:59 PM, Mark Abraham wrote: > Yanmei Song wrote: > >> Dear All: >> >> I just installed the gmx_4.0.4 double precision. >> >> When I do EM, the grompp_d command has no problem. However af

[gmx-users] Re: Energy minimization error by GMX 4.0.4

Also I have checked that it works well in gmx_3.3.3. Anyone can tell me what is the problem ? Thanks! On Wed, May 6, 2009 at 1:47 PM, Yanmei Song wrote: > Dear All: > > I just installed the gmx_4.0.4 double precision. > > When I do EM, the grompp_d command has no problem.

[gmx-users] Energy minimization error by GMX 4.0.4

/em.tpr) version 58 with version 40 program -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Error by pdb2gmx

nning the test set (available on the wiki site)? If you >> can describe your computer system (OS, version, compilers used, >> configuration options, etc.) then perhaps someone on the list can spot a >> potential pitfall. >> >> -Justin >> >> Yanmei Song wr

Re: [gmx-users] Error by pdb2gmx

ption of your hardware and > software - OS, version, compilers used, configuration options, etc, and see > if anyone can spot a problem. > > -Justin > > Yanmei Song wrote: >> >> Sorry to bother so many times. >> >> I edited the rtp and added the new residue

Re: [gmx-users] Error by pdb2gmx

4.0.4 and trying again.  If that does > not work, post to the list a complete description of your hardware and > software - OS, version, compilers used, configuration options, etc, and see > if anyone can spot a problem. > > -Justin > > Yanmei Song wrote: >> >> So

Re: [gmx-users] Error by pdb2gmx

al error: in .rtp file at line: --- Anyone knows where I did wrong? Thank you so much! On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >> >> Hi, Dallas: >> >> I added this to the ffoplsaa.rtp >>

Re: [gmx-users] Error by pdb2gmx

Hi, Justin: Thank you so much for your nice help. I will work on that according to your suggestions. On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >> >> Hi, Dallas: >> >> I added this to the ffoplsaa.rtp >> >>

Re: [gmx-users] Error by pdb2gmx

t; >> -Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Thursday, 30 April 2009 9:07 AM >> To: jalem...@vt.edu; Discussion list for GROMACS users >> Subject: Re: [gmx-u

Re: [gmx-users] Error by pdb2gmx

SI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> --- >> Program pdb2gmx,

Re: [gmx-users] Error by pdb2gmx

C 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > >> -Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx

Re: [gmx-users] Error by pdb2gmx

-Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Wednesday, 29 April 2009 8:59 AM >> To: jalem...@vt.edu; Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx

Re: [gmx-users] Error by pdb2gmx

less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >> >> Dear All users: >> >> I

[gmx-users] Error by pdb2gmx

C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 TER -- Yanmei Song Department of Chemical Engineering ASU ___

Re: [gmx-users] Non-equilibrium Viscosity Calculation

Hi, David; Thank you so much for your prompt response. Your answer is really helpful. On Mon, Apr 20, 2009 at 10:31 PM, David van der Spoel wrote: > Yanmei Song wrote: >> >>  Hi, David: >> >>  I performed the NEMD and got the following results for averaging the

Re: [gmx-users] Non-equilibrium Viscosity Calculation

1920.0001220.003688 194.440231 1940.0001220.005800 305.705505 On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Yes, I want to get the equilibrium viscosity. My question is how I can >> identify the s

Re: [gmx-users] Non-equilibrium Viscosity Calculation

Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help. On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Dear David:

Re: [gmx-users] Non-equilibrium Viscosity Calculation

e! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Dear All: >> >> I wanted to get the viscosity of my simulated polymer system. From the >> manual it said that : GROMACS also has a non-equilibrium method for >> deter

Re: [gmx-users] g_msd

gmx-users mailing list    gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx

[gmx-users] Non-equilibrium Viscosity Calculation

vance. -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

Re: [gmx-users] how to calculate the viscosity of the bulk

te the Einstein formula "by hand" from the > pressure. > > Berk > >> Date: Mon, 2 Feb 2009 19:34:59 -0500 >> From: jalem...@vt.edu >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] how to calculate the viscosity of the bulk >> >> >>

Re: [gmx-users] how to calculate the viscosity of the bulk

Einstein formula "by hand" from the > pressure. > > Berk > >> Date: Mon, 2 Feb 2009 19:34:59 -0500 >> From: jalem...@vt.edu >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] how to calculate the viscosity of the bulk >> >> >>

[gmx-users] how to calculate the viscosity of the bulk

0454 958.084 221.896 87.4938 978.044 213.811 103.699 998.004 207.287 113.678 My question is what the value should be for the viscosity of the fluid. Should I average all the values of third column to get the value. Does the value have a unit of cp? Thank you so mu

[gmx-users] Question about the pairs parameters

then should be sigma and epsi, right? Thank you so much for your answer in advance! -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS

Justin A. Lemkul : > > > Yanmei Song wrote: >> >> What makes me so confused is that I used this top for the MD run using >> ffoplsaa.itp and the there are no error message. Also I got a good >> result compared to experiment. Does it mean that what I did is totall

Re: [gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS

opls_x with the x is less than 135, then it should be OPLS UA force field right? if I want to use OPLS, How can we get the top? Thank you so much for your help! 2009/1/28 Justin A. Lemkul : > > > Yanmei Song wrote: >> >> Hi,Justin: >> >> Thanks for your response. >

Re: [gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS

parameters directly for my itp user ffoplsaa force field? Thanks a lot! 2009/1/28 Justin A. Lemkul : > > > Yanmei Song wrote: >> >> Hi, >> >> I am using ffoplsaa.itp as my force field to do a simulation using >> GROMACS. >> I have a question about how to wr

[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS

like v1 v2 v3 v4. Then my question is how can i define the dihedral parameters in itp file based on ffoplsaa force field in GROMACS? Thanks a lot! Yanmei -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users