Re: [gmx-users] periodicity and correct output

, Shuangxing Dai On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban vvcha...@gmail.com wrote: Hi, Is there an option in any gromacs utility to apply periodicity to the output configuration or trajectory? I want to get all the coordinates just within an elementary box, between 0 and LBOX in spite of any

[gmx-users] translation

. Does anyone have idea how to solve this? Thanks in advance. Thanks, Shuangxing Dai -- 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)subscribe

[gmx-users] question about dynamics

information. When I change and use Berendson for pressure coupling, there is error information and does not work. Anyone have idea about these? Thanks in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] question about dynamics

Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information? Thanks, Shuangxing Dai On Jul 12, 2010, at 15:43, Justin A. Lemkul jalem...@vt.edu wrote: Shuangxing Dai wrote: Hi

[gmx-users] pressure coupling

0.01 1.03E+00 2.12E+00 9.95E-03 1.21E-04 100 5.48359 71.5565 91.198 1.25218 300 2.62807 162.926 290.324 3.36594 500 16.6356 1048.76 492.616 5.45231 800 59.3245 594.773 799.314 9.18876 1000 80.2257 626.789 1007.23 11.2159 Thanks in advance, Shuangxing Dai -- gmx-users mailing listgmx-users

Re: [gmx-users] pressure coupling

Content-Type: text/plain; charset=UTF-8; format=flowed Shuangxing Dai wrote: Hi, all, I am trying to do anisotropic coupling using Parrinello-Rahman. I want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K

[gmx-users] anisotropic pressure coupling

= 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no It seems that the temperature coupling is fast and fluctuation is less that 1%. But the pressure coupling fails. The pressure fluctuates from +1e3 bar to -1e3 bar. Anyone can help? Thanks, Shuangxing

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84

mean if the initial pressure ( in order of GPa), object pressure is 1 bar ( 1e5 Pa). * * Thanks, Shuangxing Dai On Mon, Jun 14, 2010 at 8:50 PM, gmx-users-requ...@gromacs.org wrote: Message: 3 Date: Mon, 14 Jun 2010 19:18:14 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx

[gmx-users] anisotropic pressure coupling

in advance. Thanks, Shuangxing Dai -- 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)subscribe requests to the list. Use the www interface or send

[gmx-users] slow speed

= 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Can anyone help me? Thank you in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re: slow speed

%5BAuthor%5D . The performance there is around 1 ps/day. I do not understand why my speed is so slow and it seems that Ewald option makes it slow. Thanks, Shuangxing Dai On Thu, Apr 15, 2010 at 10:18 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx

[gmx-users] Does shell molecular exclude core shell electrostatics automatically

, Shuangxing Dai -- 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)subscribe requests to the list. Use the www interface or send it to gmx-users-requ

[gmx-users] use Xcode to debug Gromacs

Dear all, -- Shuangxing Dai ___ 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)subscribe requests

[gmx-users] use Xcode to debug Gromacs

need the breakpoints to be related with the source code so that I can trace the flow. Sorry for the last mail that I pressed space accidently... Thank you in advance. -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] how to debug a single executable file using Xcode

Dear all, I was wondering how to debug the executable file mdrun in Xcode. Right now I can debug it using gdb by following here: http://oldwiki.gromacs.org/index.php/Programmer's_Guide But I do not know how to debug it by Xcode. For example, I want to debug this command: mdrun -c steep.g96

[gmx-users] large pressure

Hi, all, I was wondering why I got large pressure after energy minimization. In MD, the pressure and pressure tensor is defined like ( equation 4.151 in manual): P=2*(E_kinetic + W)/(3*V), V is volume and W is Virial. I run a simple system, fcc gold with LJ potential to

[gmx-users] Shift electrostatic summation

in advance. -- Shuangxing Dai ___ 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)subscribe requests

Re: [gmx-users] force

Yes, I did one md step and got all non-zero forces. But for the energy minimization, all the forces are zero, althouth mdrun command gives non-zero forces. On Sun, Jun 28, 2009 at 4:23 AM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shuangxing Dai shuangxing...@gmail.com [2009-06-27

[gmx-users] force

Hi, all, I was wondering about the force given by Gromacs. One is in the .trr and .tpr file. When I read then with gmxdump, they are all zeros: traj.trr frame 0: natoms= 24000 step= 0 time=0.000e+00 lambda= 0 box (3x3): box[0]={ 3.24900e+00,

Re: [gmx-users] force

The nstfout =1 in mdout.mdp. So this should not be where the problem is. - Original Message - From: Florian Dommert domm...@icp.uni-stuttgart.de To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, June 27, 2009 3:20 PM Subject: Re: [gmx-users] force

Re: [gmx-users] force

atom at each step? Just like it did to the forces? I use this mdp file and only see the total energy for each step in the log file. Thanks again. On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shuangxing Dai shuangxing...@gmail.com [2009-06-27 18:57:41

[gmx-users] more digits

Hi, all, I need more digits to input information. But the default format of pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or is there any other direct ways to input more digits coordinate information in Gromacs? Thanks in advance. Shuangxing

[gmx-users] Shift Electrostatic Summation

Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) (

Re: [gmx-users] Shift Electrostatic Summation

in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? Thank you for your help. Shuangxing Dai - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx

Re: [gmx-users] Shift Electrostatic Summation

- Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 14 April, 2009 8:01 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user

[gmx-users] shell molecular dynamics

Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? 2. What does the 1 in [ polarization ] part mean in sw.itp? 3. Is it

Re: [gmx-users] shell molecular dynamics

is the problem. Shuangxing Dai - Original Message - From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 13 April, 2009 11:15 AM Subject: Re: [gmx-users] shell molecular dynamics Shuangxing Dai wrote: Hi, all, I am doing

Re: [gmx-users] How to add another electrostatic summation methodin Gromacs

for your kindly help. Shuangxing Dai - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 26 March, 2009 4:56 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodin Gromacs

Re: [gmx-users] How to add another electrostatic summation methodinGromacs

- Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 27 March, 2009 5:01 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai wrote: Yes, but I still

Re: [gmx-users] How to add another electrostatic summation method in Gromacs

this Wolf method can, so I cannot simply use Gromacs to do my simulation. The question is which files needed to be modified if I want to add a new one? Is there any direct way? Or I should read all the whole code? Thank you very much. Shuangxing Dai On Mon, Mar 23, 2009 at 11:55 PM, Mark Abraham

[gmx-users] How to add another electrostatic summation method in Gromacs

Hi, all, I was wondering how to add another electrostatic summation method--Wolf summation into Gromacs. Wolf summation is a treatment for summation of Coulombic energy. Since the formula of total potential energy for each ion is known, how to add this into Gromacs? According to Chapter 7,

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

aboutthecombinationrules Shuangxing Dai wrote: Yes, add parameters for crystalline zinc oxide, which require Buckingham nonbonded interactions, that is what I am doing. I think I have changed all the necessary parts for the Buckingham potential. Is there any direct way to accomplish my goal

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

Abraham mark.abra...@anu.edu.au Shuangxing Dai wrote: No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines of error informaion like this: ERROR 77 [file ffgmxnb.itp, line 144]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) Sure

Re: [gmx-users] combination rules -- the part aboutthe combinationrules

Sent: Friday, February 20, 2009 6:02 PM Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules Shuangxing Dai wrote: Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; ij func abc6 Zn O2

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

@gromacs.org Sent: Friday, February 20, 2009 6:02 PM Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules Shuangxing Dai wrote: Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; i j func a b c6 Zn O 2

Re: [gmx-users] combination rules -- the part about the combinationrules

Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; ij func abc6 Zn O2 ... . But error occured.. ERROR 1 [file ffgmxnb.itp, line 270]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[gmx-users] combination rules

Hello, I was wondering how to set up parameters for interactions between two different atoms A and B. Since for Gromacs parameters are defined to each kind of atom, I cannot specify parameters between A and B. For Buckingham potential, the rule was: A_ij=(A_ii * A_jj)^(1/2) So anyone

[gmx-users] new atom type and force field

Hi, all gmx users: I am doing a simulation with NaCl (and ZnO, GaN). I start with the .pdb file. But the Gromacs cannot recognize my new atom, such as Na, Cl. How to add new atoms to Gromacs? I am going to use periodical boundary conditions and LJ potential, shell model , apply