Re: [gmx-users] Re: local pressure v4.5 issues

Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give this tpr file to v4.0.2_local_pressure to rerun the simulation. Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users

Re: [gmx-users] Re: local pressure v4.5 issues

I have tried CHARMM FF in v4.0.4 and it does not give error, so it seems dihedral type 9 has already been implemented in v4.0.4. Jianguo From: Jianguo Li ljg...@yahoo.com.sg To: Amit Choubey kgp.a...@gmail.com Cc: Discussion list for GROMACS users

[gmx-users] g_tune_pme

Hi everyone, please I was running simulations with gromacs version 4.0.3 ,but I got the following error: Average load imbalance: 12.1 % Part of the total run time spent waiting due to load imbalance: 6.9 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 9 %

Re: [gmx-users] g_tune_pme

Hi Carla, On Jul 28, 2011, at 9:38 AM, Carla Jamous wrote: Hi everyone, please I was running simulations with gromacs version 4.0.3 ,but I got the following error: Average load imbalance: 12.1 % Part of the total run time spent waiting due to load imbalance: 6.9 % Steps where the load

Re: [gmx-users] Conversion of the GLYCAM dihedral parameters

Hi SA, I think this is due to the original amb2gmx.pl coder only considering AMBER type dihedrals. He/She didn't expect any negative values. You'll notice certain groups like NAc and COO- on sugars are affected when you run your simulation. Below is a similar post with a fix to the amb2gmx.pl

Re: [gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: I doubt the chain identifiers are relevant. Both .gro and .pdb files should display properly. The only odd instance I can think of is that without separate chains, some programs may interpret the protein coordinates as a single molecule, but I would think that

[gmx-users] Implicit Water Simulation

Hi, I am trying to run a simulation with implicit water on explicit ions - Na, CL to see the disassembly of NaCL. I get the following error message: GB parameter(s) missing or negative for atom type 'opls_401' GB parameter(s) missing or negative for atom type 'opls_407' Is it possible to run this

[gmx-users] Re: multiple protein interaction

hi, According to the help frm gmx-users , I did editconf with -center option twice.concatenated the coordinate files using cat. Then i ran frm pdb2gmx till genbox..When I saw result pdb using pymol there was only one protein inside the box.Why is it like that?When i opened the gro file after

Re: [gmx-users] Implicit Water Simulation

ifat shub wrote: Hi, I am trying to run a simulation with implicit water on explicit ions - Na, CL to see the disassembly of NaCL. I get the following error message: GB parameter(s) missing or negative for atom type 'opls_401' GB parameter(s) missing or negative for atom type 'opls_407' Is

Re: [gmx-users] Re: multiple protein interaction

smriti Sebastian wrote: hi, According to the help frm gmx-users , I did editconf with -center option twice.concatenated the coordinate files using cat. Then i ran frm pdb2gmx till genbox..When I saw result pdb using pymol there was only one protein inside the box.Why is it like that?When i

[gmx-users] Fatal error: file type out of range (48)

Hi, Please does anyone Know what this error means? Fatal error: file type out of range (48) Here's my script: #PBS -S /bin/bash #PBS -N job_md6ns #PBS -e job_md6ns.err #PBS -o job_md6ns.log #PBS -m ae -M carlajam...@gmail.com #PBS -l select=2:ncpus=8:mpiprocs=8 #PBS -l walltime=024:00:00 cd

Re: [gmx-users] Fatal error: file type out of range (48)

Carla Jamous wrote: Hi, Please does anyone Know what this error means? Fatal error: file type out of range (48) Here's my script: #PBS -S /bin/bash #PBS -N job_md6ns #PBS -e job_md6ns.err #PBS -o job_md6ns.log #PBS -m ae -M carlajam...@gmail.com mailto:carlajam...@gmail.com #PBS -l

[gmx-users] RE: g_clustsize

Dear Stefano, I forward your question to the gromacs-users mailing list. Please send further inquiries there - there may be people more qualified than me to reply (unless you refer to my modified version or to one of my papers) I'm not sure if the .xpm files give the information you're

[gmx-users] disulfide bond, molecule type

/ // I doubt the chain identifiers are relevant. Both .gro and .pdb files should // display properly. The only odd instance I can think of is that without separate // chains, some programs may interpret the protein coordinates as a single // molecule, but I would think that would only

Re: [gmx-users] Re: local pressure v4.5 issues

I just checked that the mdrun of v4.0.2_local_pressure can read the tpr generated from grompp of v4.0.7. I did get some local pressure numbers. Also i checked the potential energy between 4.0.2 and 4.0.7 there is a difference of about 0.0008% . I am just wondering how this problem got fixed ie

Re: [gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: / // I doubt the chain identifiers are relevant. Both .gro and .pdb files should // display properly. The only odd instance I can think of is that without separate // chains, some programs may interpret the protein coordinates as a single // molecule, but I would

Re: [gmx-users] Re: local pressure v4.5 issues

Amit Choubey wrote: I just checked that the mdrun of v4.0.2_local_pressure can read the tpr generated from grompp of v4.0.7. I did get some local pressure numbers. Also i checked the potential energy between 4.0.2 and 4.0.7 there is a difference of about 0.0008% . I am just wondering how

[gmx-users] limit in reducing time step for integration

Hi, I have been making some tests reducting the time step for the integration with md in the grompp.mdp file and observed that obtained results differ when the time step is 0.0001 from those obtained for time steps 0.0005 and 0.001. Do you have any idea of which can be the problem? Thanks,

Re: [gmx-users] limit in reducing time step for integration

María Paula Longinotti wrote: Hi, I have been making some tests reducting the time step for the integration with md in the grompp.mdp file and observed that obtained results differ when the time step is 0.0001 from those obtained for time steps 0.0005 and 0.001. Do you have any idea of

[gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water

Hi, Thank you. I tried again, this time doing 100 ps of NVT equlibration, followed by 500 ps of NVE. I have posted my results here: http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf But, they are not much better. For the NVT equilibration, I used v-rescale temperature coupling with

[gmx-users] zero charge model- simulation time

Hello, I set zero charges to all atoms using the commands below: grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v So before doing mdrun md I add tpbconv command and use the out put *-ZERO_md.tpr for the mdrun md

Re: [gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water

Andrew DeYoung wrote: Hi, Thank you. I tried again, this time doing 100 ps of NVT equlibration, followed by 500 ps of NVE. I have posted my results here: http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf But, they are not much better. For the NVT equilibration, I used v-rescale

Re: [gmx-users] zero charge model- simulation time

Juliette N. wrote: Hello, I set zero charges to all atoms using the commands below: grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v So before doing mdrun md I add tpbconv command and use the out put

[gmx-users] ignore H-bond

Deer users. I want to ignore the hydrogen bonds in water. My system consists of ions and water molecules. Is there any way ignore hydrogen bonding of water ? Regards saeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] zero charge model- simulation time

Juliette N. wrote: Thanks Justin. One last question, I wanted to make sure if zetting zero charge using tpbconv is identical to setting zero charges in top file. Yes. Verify the contents of your .tpr file with gmxdump. I am concerned about the model to be inaccurate. Do these two models

Re: [gmx-users] ignore H-bond

Saeid Akbarshahi wrote: Deer users. I want to ignore the hydrogen bonds in water. In analysis, or during MD? My system consists of ions and water molecules. Is there any way ignore hydrogen bonding of water ? Depends on the answer to the question above. During MD, no. During analysis

Re: [gmx-users] zero charge model- simulation time

Hi again, I am wondering if using tpbconv to set zero charges (case 1) works similar to when one sets zero atom charges in topology file from the very beginning (case 2). Do these two cases work similarly? I checked tpr file and I see that charges are set to zero. Can you please tell me what

[gmx-users] minor trjconv issue

Hi all, When i use the following trjconv_without_shock -f all_molecules_500ns_fixedpbc.gro -o traj.gro -novel -s npt.tpr traj.gro still has velocities. Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] minor trjconv issue

Amit Choubey wrote: Hi all, When i use the following trjconv_without_shock -f all_molecules_500ns_fixedpbc.gro -o traj.gro -novel -s npt.tpr traj.gro still has velocities. Please file an issue report on redmine.gromacs.org so it can be fixed. I know I've seen this reported before,

Re: [gmx-users] zero charge model- simulation time

Juliette N. wrote: Hi again, I am wondering if using tpbconv to set zero charges (case 1) works similar to when one sets zero atom charges in topology file from the very beginning (case 2). Do these two cases work similarly? They should work identically. I checked tpr file and I see

Re: [gmx-users] minor trjconv issue

done On Thu, Jul 28, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: Hi all, When i use the following trjconv_without_shock -f all_molecules_500ns_fixedpbc.**gro -o traj.gro -novel -s npt.tpr traj.gro still has velocities. Please file an issue report

[gmx-users] need help with topology file

Hi, I am trying to use two types of force fields for my system which has protein and fullerene. i want to use OPLS for protein and ffG53a6 for fullerene(as i don't have opls readily available for this). When i use two itp files in #include section grompp does not allow me to do that with the

RE: [gmx-users] limit in reducing time step for integration

The oscilations in pressure are different, they are much bigger for an integration time of 0.0001than for integration times of 0.001 or 0.0005. Date: Thu, 28 Jul 2011 12:27:19 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] limit in reducing time step for

Re: [gmx-users] need help with topology file

jampani srinivas wrote: Hi, I am trying to use two types of force fields for my system which has protein and fullerene. i want to use OPLS for protein and ffG53a6 for fullerene(as i don't have opls readily available for this). When i use two itp files in #include section grompp does not

Re: [gmx-users] limit in reducing time step for integration

María Paula Longinotti wrote: The oscilations in pressure are different, they are much bigger for an integration time of 0.0001than for integration times of 0.001 or 0.0005. I wouldn't base any conclusion on pressure or the fluctuations therein. These quantities are extremely sensitive

Re: [gmx-users] zero charge model- simulation time

Hello Justin, I am using tpbconv to set zero charges after em and after doing grompp_md. grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v Do I need to use tpbconv after grompp_em? (before mdrun_em) Regards, On 28

Re: [gmx-users] zero charge model- simulation time

Juliette N. wrote: Hello Justin, I am using tpbconv to set zero charges after em and after doing grompp_md. grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v Do I need to use tpbconv after grompp_em? (before

[gmx-users] Re: hi Gromacs error

Please add the attached file to the gromos43a1p.ff directory. -Justin kalai arasan wrote: justin, I am sorry to disturb you again, i just like to convey the information i got another error while using version 4.5.3

Re: [gmx-users] Re: hi Gromacs error

Sorry all, disregard this. It was intended to be sent to someone else. Stupid email autocompletion... -Justin Justin A. Lemkul wrote: Please add the attached file to the gromos43a1p.ff directory. -Justin kalai arasan wrote: justin, I am sorry to disturb you again, i just like

Re: [gmx-users] zero charge model- simulation time

sorry Justin to get back to you gain. This means I have to set zero charges twice ( after grompp EM and grommp MD), since in grompp_md I am using topology file which sets actual charges again to all atoms. Do atoms charges affect EM configuration ? Regards, On 28 July 2011 17:44, Justin A.

Re: Re: [gmx-users] zero charge model- simulation time

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Re: [gmx-users] zero charge model- simulation time

Juliette N. wrote: sorry Justin to get back to you gain. This means I have to set zero charges twice ( after grompp EM and grommp MD), since in grompp_md I am using topology file which sets actual charges again to all atoms. Do atoms charges affect EM configuration ? Anything that

[gmx-users] disulfide bond, molecule type

No. You said before you had broken chains. Applying trjconv -pbc mol fixes this issue. Molecules can be broken across periodic boundaries and is an entirely normal phenomenon. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions / And I tried another way. // I

[gmx-users] Arginine_Hydrochloride topology

Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. shahid Nayeem --