Re: [gmx-users] Potential Energy

Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Yanmei Song yson...@asu.edu 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: I finally

[gmx-users] Potential Energy

, the 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

Re: [gmx-users] Potential Energy

: Yanmei Song wrote: Dear Justin: Sorry, that itp is the original one generated by PRODRG. Also I have modified it based on a optimized force field of the molecule. (See attached file and the literature of the force field). But still the potential energy is positively 1e2 and why the system

[gmx-users] OPLS force field

will be 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't

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

Spoel sp...@xray.bmc.uu.sewrote: 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 length ranged from 0.9 to 1.5

[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 post (un

[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 post (un

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

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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: Anyone knows how to get the standard errors of the results based on block averaging from non-equilibrium MD

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

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 jalem...@vt.edu wrote: Yanmei Song wrote

[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

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 sp...@xray.bmc.uu.sewrote: Yanmei Song wrote: Dear All

[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

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

for 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?

A. Lemkul jalem...@vt.edu 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 constraints = all_bonds integrator = md dt

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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics

[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

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 Department of Chemical Engineering Arizona State University -- Express yourself instantly

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

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 Department of Chemical Engineering Arizona State

[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

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 to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under

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 yson...@asu.edu wrote

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

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 ffoplsaabon.itp. it doesn't include any dihedral consisting of SI

[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] shift function for vdwtype and density

. Thanks! On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: 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 remain unchanged. For example

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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear

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 jalem...@vt.edu 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 results for pure water bulk system

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

. 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: 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

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

the 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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Thanks for your response. Here

[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

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

of 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 phi and k for function 1 for periodic type. I wanted to use OPLS

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

...@vt.edu 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 potential. Is there any way I can get

[gmx-users] Pressure coupling and cut-off

. 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 Engineering Arizona

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

is 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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800

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

be 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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Sorry to bother so many times. After EM everything looks fine. However the mdrun died with the error

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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear users: I set up a 8nm cubic box with 6 long chain molecules. After EM

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

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 residue:43 I was thinking the problem may not come from the artifact of visualization. Since if the gro file

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

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/search

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 mark.abra...@anu.edu.auwrote: 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 after I submit the job

Re: [gmx-users] Error by pdb2gmx

)? 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 wrote: Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run

Re: [gmx-users] Error by pdb2gmx

, 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 as following, which I think should be no problem. [ PDM ]  [ atoms ]    SI1    SI

Re: [gmx-users] Error by pdb2gmx

...@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-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ]  [ atoms ]     SI

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 jalem...@vt.edu wrote: Yanmei Song wrote: Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ]      SI       SI

Re: [gmx-users] Error by pdb2gmx

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: Sorry to bother so many times. I edited the rtp and added the new

Re: [gmx-users] Error by pdb2gmx

...@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-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29

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 jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3

[gmx-users] Error by pdb2gmx

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 ___ gmx-users

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 jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long

Re: [gmx-users] Error by pdb2gmx

-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 Dear Justin: Do you have any suggestions on how I can get the itp

Re: [gmx-users] g_msd

before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU

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

, Apr 16, 2009 at 11:33 PM, David van der Spoel sp...@xray.bmc.uu.se 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 determining the viscosity (page 123) Does this mean

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 sp...@xray.bmc.uu.se wrote: Yanmei Song wrote: Dear David

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 sp...@xray.bmc.uu.se wrote: Yanmei Song wrote: Yes, I want to get the equilibrium viscosity. My question is how I can identify the system

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 sp...@xray.bmc.uu.se wrote: Yanmei Song wrote:  Hi, David:  I performed the NEMD and got the following results for averaging the last 1 ns. So

[gmx-users] Non-equilibrium Viscosity Calculation

. -- 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't post (un

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

. 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 Yanmei Song wrote: Hi, Justin: I saw in the manual that by g_energy -vis the viscosity of the system can be calculated

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

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 Yanmei Song wrote: Hi, Justin: I saw in the manual that by g_energy -vis the viscosity of the system can

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

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 much in advance! Yanmei Song Department of Chemical Engineering ASU

[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

[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

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

these parameters directly for my itp user ffoplsaa force field? Thanks a lot! 2009/1/28 Justin A. Lemkul jalem...@vt.edu: 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 write the parameters in dihedrals in the itp

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

Justin A. Lemkul jalem...@vt.edu: 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 totally wrong with using this top