date:20190412

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash

Thank you Justin and Mark, it worked. I will bare all this in mind.

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Justin Lemkul
Sent: 12 April 2019 16:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters



On 4/12/19 11:57 AM, Pandya, Akash wrote:
> How would I find out if there are duplicates or not?

grompp has told you what it is finding as duplicates. You need to look into the 
parent force field files and compare the values you are supplying vs. what are 
in the existing force field, particularly for the atom types. grompp has 
already told you the existing (force field) and new (your topology) values.

-Justin

> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  On Behalf Of Mark 
> Abraham
> Sent: 12 April 2019 16:47
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Citrate parameters
>
> Hi,
>
> It seems that all/most things before the [moleculetype] definition duplicates 
> the standard contents of the forcefield, as you can see from the contents of 
> the itp file and the original warnings you mentioned.
> Unfortunately you now have the problem of determining whether all of it is 
> duplication, or only some of it.
>
> Mark
>
> On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, 
> 
> wrote:
>
>> Sorry but I don't quite understand where the duplicates come from?
>> I've pasted my itp file below:
>>
>> [ defaults ]
>> 1 2 yes 1.0 1.0
>>
>> [ atomtypes ]
>> OC  8 15. -0.760 A 0.302906 0.50208 CC  6 12.0110  0.620 A
>> 0.356359 0.29288 HA  1  1.0080  0.090 A 0.235197 0.09205
>> CT2 6 12.0110 -0.180 A 0.387541 0.23012 CT  6 12.0110 -0.070 A
>> 0.405359 0.08368
>> OH1 8 15. -0.540 A 0.315378 0.63639
>> H   1  1.0080  0.310 A 0.040001 0.19623
>>
>> [ bondtypes ]
>> CC OC  1  0.126 439320.0
>> CC CT2 1  0.152 167360.0
>> CT2HA  1  0.111 258571.2
>> OH1H   1  0.096 456056.0
>> CT CC  1  0.152 167360.0
>> CT2CT  1  0.150 186188.0
>> CT OH1 1  0.142 358150.4
>>
>> [ angletypes ]
>> OCCCOC  5 124.00   836.80   0.2225   58576.000
>> OCCC   CT2  5 118.00   334.72   0.2388   41840.000
>> CC   CT2HA  5 109.50   276.14   0.2163   25104.000
>> HA   CT2HA  5 109.00   297.06   0.18024518.720
>> CTCCOC  5 118.00   334.72   0.2388   41840.000
>> CT2   CTCC  5 108.00   435.14   0.   0.000
>> CT2   CT   CT2  5 113.60   488.27   0.25619338.688
>> HA   CT2CT  5 110.10   279.74   0.2179   18853.104
>> CC   CT2CT  5 108.00   435.14   0.   0.000
>> CT2   CT   OH1  5 110.10   633.46   0.   0.000
>> OH1   CTCC  5 110.10   633.46   0.   0.000
>> CT   OH1 H  5 106.00   481.16   0.   0.000
>>
>> [ dihedraltypes ]
>> HA   CT2CC   OC  9   180.00   0.2092 6
>> CT   CT2CC   OC  9   180.00   0.2092 6
>> CT2   CT   CT2   CC  9 0.00   4. 3
>> OH1   CT   CT2   CC  9 0.00   0.8368 3
>> OH1   CT   CT2   HA  9 0.00   0.8368 3
>> CCCT   CT2   CC  9 0.00   0.8368 3
>> CCCT   CT2   HA  9 0.00   0.8368 3
>> CT2   CT   CT2   HA  9 0.00   0.8368 3
>> OH1   CTCC   OC  9 0.00   1.2000 2
>> CT2   CTCC   OC  9   180.00   0.2092 6
>> CCCT   OH1H  9 0.00   0.2092 1
>> CT2   CT   OH1H  9 0.00   0.5858 3
>> CC   CT2OC   OC  2 0.00  803.328
>> CCCTOC   OC  2 0.00  803.328
>>
>> [ moleculetype ]
>> CIT 3
>>
>> [ atoms ]
>> 1   CC   1  CIT   C  1   0.62012.011
>> 2   CT2  1  CIT   C  2  -0.18012.011
>> 3   CT   1  CIT   C  3  -0.07012.011
>> 4   CC   1  CIT   C  4   0.62012.011
>> 5   CT2  1  CIT   C  5  -0.18012.011
>> 6   CC   1  CIT   C  6   0.62012.011
>> 7   OC   1  CIT   O  7  -0.76015.999
>> 8   OC   1  CIT   O  8  -0.76015.999
>> 9   OC   1  CIT   O  9  -0.76015.999
>> 10  OC   1  CIT   O 10  -0.76015.999
>> 11  OC   1  CIT   O 11  -0.76015.999
>> 12  OC   1  CIT   O 12  -0.76015.999
>> 13  OH1  1  CIT   O 13  -0.54015.999
>> 14  HA   1  CIT   H 14   0.090 1.008
>> 15  HA   1  CIT   H 15   0.090 1.008
>> 16  HA   1  CIT   H 16   0.090 1.008
>> 17  HA   1  CIT   H 17   0.090 1.008
>> 18  H1  CIT   H 18   0.310 1.008
>>
>> [ bonds ]
>> 1 81
>> 1 71
>> 1 2   1
>> 2 15   1
>> 2 14   1
>> 2 31
>> 3 13   1
>> 3 51
>> 3 41
>> 4 10   1
>> 4 91
>> 5 17   1
>> 5 16   1
>> 5 61
>> 6 12   1
>> 6 11   1
>> 13 18  1
>> [ angles ]
>> 8 1 7   5
>> 8 1 2   5
>> 7 1 2   5
>> 1 215   5
>> 15214   5
>> 152 3   5
>> 1 214   5
>> 142 3   5
>> 1 2 3   5
>> 2 313   5
>> 133 5   5
>> 133 4   5
>> 2 3 5   5
>> 5 3 4   5
>> 2 3 4   5
>> 3 410   5
>> 104 9   5
>> 3 4 9   5
>> 3 517   5
>> 17516   5
>> 175 6   5
>> 3 516   5
>>

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Justin Lemkul





On 4/12/19 11:57 AM, Pandya, Akash wrote:

How would I find out if there are duplicates or not?


grompp has told you what it is finding as duplicates. You need to look 
into the parent force field files and compare the values you are 
supplying vs. what are in the existing force field, particularly for the 
atom types. grompp has already told you the existing (force field) and 
new (your topology) values.


-Justin


Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Mark Abraham
Sent: 12 April 2019 16:47
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Citrate parameters

Hi,

It seems that all/most things before the [moleculetype] definition duplicates 
the standard contents of the forcefield, as you can see from the contents of 
the itp file and the original warnings you mentioned.
Unfortunately you now have the problem of determining whether all of it is 
duplication, or only some of it.

Mark

On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, 
wrote:


Sorry but I don't quite understand where the duplicates come from?
I've pasted my itp file below:

[ defaults ]
1 2 yes 1.0 1.0

[ atomtypes ]
OC  8 15. -0.760 A 0.302906 0.50208 CC  6 12.0110  0.620 A
0.356359 0.29288 HA  1  1.0080  0.090 A 0.235197 0.09205
CT2 6 12.0110 -0.180 A 0.387541 0.23012 CT  6 12.0110 -0.070 A
0.405359 0.08368
OH1 8 15. -0.540 A 0.315378 0.63639
H   1  1.0080  0.310 A 0.040001 0.19623

[ bondtypes ]
CC OC  1  0.126 439320.0
CC CT2 1  0.152 167360.0
CT2HA  1  0.111 258571.2
OH1H   1  0.096 456056.0
CT CC  1  0.152 167360.0
CT2CT  1  0.150 186188.0
CT OH1 1  0.142 358150.4

[ angletypes ]
OCCCOC  5 124.00   836.80   0.2225   58576.000
OCCC   CT2  5 118.00   334.72   0.2388   41840.000
CC   CT2HA  5 109.50   276.14   0.2163   25104.000
HA   CT2HA  5 109.00   297.06   0.18024518.720
CTCCOC  5 118.00   334.72   0.2388   41840.000
CT2   CTCC  5 108.00   435.14   0.   0.000
CT2   CT   CT2  5 113.60   488.27   0.25619338.688
HA   CT2CT  5 110.10   279.74   0.2179   18853.104
CC   CT2CT  5 108.00   435.14   0.   0.000
CT2   CT   OH1  5 110.10   633.46   0.   0.000
OH1   CTCC  5 110.10   633.46   0.   0.000
CT   OH1 H  5 106.00   481.16   0.   0.000

[ dihedraltypes ]
HA   CT2CC   OC  9   180.00   0.2092 6
CT   CT2CC   OC  9   180.00   0.2092 6
CT2   CT   CT2   CC  9 0.00   4. 3
OH1   CT   CT2   CC  9 0.00   0.8368 3
OH1   CT   CT2   HA  9 0.00   0.8368 3
CCCT   CT2   CC  9 0.00   0.8368 3
CCCT   CT2   HA  9 0.00   0.8368 3
CT2   CT   CT2   HA  9 0.00   0.8368 3
OH1   CTCC   OC  9 0.00   1.2000 2
CT2   CTCC   OC  9   180.00   0.2092 6
CCCT   OH1H  9 0.00   0.2092 1
CT2   CT   OH1H  9 0.00   0.5858 3
CC   CT2OC   OC  2 0.00  803.328
CCCTOC   OC  2 0.00  803.328

[ moleculetype ]
CIT 3

[ atoms ]
1   CC   1  CIT   C  1   0.62012.011
2   CT2  1  CIT   C  2  -0.18012.011
3   CT   1  CIT   C  3  -0.07012.011
4   CC   1  CIT   C  4   0.62012.011
5   CT2  1  CIT   C  5  -0.18012.011
6   CC   1  CIT   C  6   0.62012.011
7   OC   1  CIT   O  7  -0.76015.999
8   OC   1  CIT   O  8  -0.76015.999
9   OC   1  CIT   O  9  -0.76015.999
10  OC   1  CIT   O 10  -0.76015.999
11  OC   1  CIT   O 11  -0.76015.999
12  OC   1  CIT   O 12  -0.76015.999
13  OH1  1  CIT   O 13  -0.54015.999
14  HA   1  CIT   H 14   0.090 1.008
15  HA   1  CIT   H 15   0.090 1.008
16  HA   1  CIT   H 16   0.090 1.008
17  HA   1  CIT   H 17   0.090 1.008
18  H1  CIT   H 18   0.310 1.008

[ bonds ]
1 81
1 71
1 2   1
2 15   1
2 14   1
2 31
3 13   1
3 51
3 41
4 10   1
4 91
5 17   1
5 16   1
5 61
6 12   1
6 11   1
13 18  1
[ angles ]
8 1 7   5
8 1 2   5
7 1 2   5
1 215   5
15214   5
152 3   5
1 214   5
142 3   5
1 2 3   5
2 313   5
133 5   5
133 4   5
2 3 5   5
5 3 4   5
2 3 4   5
3 410   5
104 9   5
3 4 9   5
3 517   5
17516   5
175 6   5
3 516   5
165 6   5
3 5 6   5
5 612   5
12611   5
5 611   5
31318   5

[ exclusions ]
18  9 10

[ pairs ]
10 18 2 0.3 -0.760 0.310 0.17145 0.310857
9  18 2 0.3 -0.760 0.310 0.17145 0.310857

[ dihedrals ]
812   15  9
712   15  9
812   14  9
712   14  9
8123  9
7123  9
123   13  9
15   23   13  9
14   23   13  9
1235  9
15   235  9
14   235  9
1234  9
15   234  9
14   234  9
23   13   18  9
53   13   18  9
43   13   18  9
235   17  9
13   35   17  9
435   17  9
23

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash

How would I find out if there are duplicates or not? 

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Mark Abraham
Sent: 12 April 2019 16:47
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Citrate parameters

Hi,

It seems that all/most things before the [moleculetype] definition duplicates 
the standard contents of the forcefield, as you can see from the contents of 
the itp file and the original warnings you mentioned.
Unfortunately you now have the problem of determining whether all of it is 
duplication, or only some of it.

Mark

On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, 
wrote:

> Sorry but I don't quite understand where the duplicates come from? 
> I've pasted my itp file below:
>
> [ defaults ]
> 1 2 yes 1.0 1.0
>
> [ atomtypes ]
> OC  8 15. -0.760 A 0.302906 0.50208 CC  6 12.0110  0.620 A 
> 0.356359 0.29288 HA  1  1.0080  0.090 A 0.235197 0.09205
> CT2 6 12.0110 -0.180 A 0.387541 0.23012 CT  6 12.0110 -0.070 A 
> 0.405359 0.08368
> OH1 8 15. -0.540 A 0.315378 0.63639
> H   1  1.0080  0.310 A 0.040001 0.19623
>
> [ bondtypes ]
> CC OC  1  0.126 439320.0
> CC CT2 1  0.152 167360.0
> CT2HA  1  0.111 258571.2
> OH1H   1  0.096 456056.0
> CT CC  1  0.152 167360.0
> CT2CT  1  0.150 186188.0
> CT OH1 1  0.142 358150.4
>
> [ angletypes ]
> OCCCOC  5 124.00   836.80   0.2225   58576.000
> OCCC   CT2  5 118.00   334.72   0.2388   41840.000
> CC   CT2HA  5 109.50   276.14   0.2163   25104.000
> HA   CT2HA  5 109.00   297.06   0.18024518.720
> CTCCOC  5 118.00   334.72   0.2388   41840.000
> CT2   CTCC  5 108.00   435.14   0.   0.000
> CT2   CT   CT2  5 113.60   488.27   0.25619338.688
> HA   CT2CT  5 110.10   279.74   0.2179   18853.104
> CC   CT2CT  5 108.00   435.14   0.   0.000
> CT2   CT   OH1  5 110.10   633.46   0.   0.000
> OH1   CTCC  5 110.10   633.46   0.   0.000
> CT   OH1 H  5 106.00   481.16   0.   0.000
>
> [ dihedraltypes ]
> HA   CT2CC   OC  9   180.00   0.2092 6
> CT   CT2CC   OC  9   180.00   0.2092 6
> CT2   CT   CT2   CC  9 0.00   4. 3
> OH1   CT   CT2   CC  9 0.00   0.8368 3
> OH1   CT   CT2   HA  9 0.00   0.8368 3
> CCCT   CT2   CC  9 0.00   0.8368 3
> CCCT   CT2   HA  9 0.00   0.8368 3
> CT2   CT   CT2   HA  9 0.00   0.8368 3
> OH1   CTCC   OC  9 0.00   1.2000 2
> CT2   CTCC   OC  9   180.00   0.2092 6
> CCCT   OH1H  9 0.00   0.2092 1
> CT2   CT   OH1H  9 0.00   0.5858 3
> CC   CT2OC   OC  2 0.00  803.328
> CCCTOC   OC  2 0.00  803.328
>
> [ moleculetype ]
> CIT 3
>
> [ atoms ]
> 1   CC   1  CIT   C  1   0.62012.011
> 2   CT2  1  CIT   C  2  -0.18012.011
> 3   CT   1  CIT   C  3  -0.07012.011
> 4   CC   1  CIT   C  4   0.62012.011
> 5   CT2  1  CIT   C  5  -0.18012.011
> 6   CC   1  CIT   C  6   0.62012.011
> 7   OC   1  CIT   O  7  -0.76015.999
> 8   OC   1  CIT   O  8  -0.76015.999
> 9   OC   1  CIT   O  9  -0.76015.999
> 10  OC   1  CIT   O 10  -0.76015.999
> 11  OC   1  CIT   O 11  -0.76015.999
> 12  OC   1  CIT   O 12  -0.76015.999
> 13  OH1  1  CIT   O 13  -0.54015.999
> 14  HA   1  CIT   H 14   0.090 1.008
> 15  HA   1  CIT   H 15   0.090 1.008
> 16  HA   1  CIT   H 16   0.090 1.008
> 17  HA   1  CIT   H 17   0.090 1.008
> 18  H1  CIT   H 18   0.310 1.008
>
> [ bonds ]
> 1 81
> 1 71
> 1 2   1
> 2 15   1
> 2 14   1
> 2 31
> 3 13   1
> 3 51
> 3 41
> 4 10   1
> 4 91
> 5 17   1
> 5 16   1
> 5 61
> 6 12   1
> 6 11   1
> 13 18  1
> [ angles ]
> 8 1 7   5
> 8 1 2   5
> 7 1 2   5
> 1 215   5
> 15214   5
> 152 3   5
> 1 214   5
> 142 3   5
> 1 2 3   5
> 2 313   5
> 133 5   5
> 133 4   5
> 2 3 5   5
> 5 3 4   5
> 2 3 4   5
> 3 410   5
> 104 9   5
> 3 4 9   5
> 3 517   5
> 17516   5
> 175 6   5
> 3 516   5
> 165 6   5
> 3 5 6   5
> 5 612   5
> 12611   5
> 5 611   5
> 31318   5
>
> [ exclusions ]
> 18  9 10
>
> [ pairs ]
> 10 18 2 0.3 -0.760 0.310 0.17145 0.310857
> 9  18 2 0.3 -0.760 0.310 0.17145 0.310857
>
> [ dihedrals ]
> 812   15  9
> 712   15  9
> 812   14  9
> 712   14  9
> 8123  9
> 7123  9
> 123   13  9
> 15   23   13  9
> 14   23   13  9
> 1235  9
> 15   235  9
> 14   235  9
> 1234  9
> 15   234  9
> 14   234  9
> 23   13   18  9
> 53   13   18  9
> 43   13   18  9
> 235   17  9
> 13   35   17  9
> 435   17  9
> 235   16  9
> 13   35   16  9
> 435   16  9
> 235

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Mark Abraham

Hi,

It seems that all/most things before the [moleculetype] definition
duplicates the standard contents of the forcefield, as you can see from the
contents of the itp file and the original warnings you mentioned.
Unfortunately you now have the problem of determining whether all of it is
duplication, or only some of it.

Mark

On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, 
wrote:

> Sorry but I don't quite understand where the duplicates come from? I've
> pasted my itp file below:
>
> [ defaults ]
> 1 2 yes 1.0 1.0
>
> [ atomtypes ]
> OC  8 15. -0.760 A 0.302906 0.50208
> CC  6 12.0110  0.620 A 0.356359 0.29288
> HA  1  1.0080  0.090 A 0.235197 0.09205
> CT2 6 12.0110 -0.180 A 0.387541 0.23012
> CT  6 12.0110 -0.070 A 0.405359 0.08368
> OH1 8 15. -0.540 A 0.315378 0.63639
> H   1  1.0080  0.310 A 0.040001 0.19623
>
> [ bondtypes ]
> CC OC  1  0.126 439320.0
> CC CT2 1  0.152 167360.0
> CT2HA  1  0.111 258571.2
> OH1H   1  0.096 456056.0
> CT CC  1  0.152 167360.0
> CT2CT  1  0.150 186188.0
> CT OH1 1  0.142 358150.4
>
> [ angletypes ]
> OCCCOC  5 124.00   836.80   0.2225   58576.000
> OCCC   CT2  5 118.00   334.72   0.2388   41840.000
> CC   CT2HA  5 109.50   276.14   0.2163   25104.000
> HA   CT2HA  5 109.00   297.06   0.18024518.720
> CTCCOC  5 118.00   334.72   0.2388   41840.000
> CT2   CTCC  5 108.00   435.14   0.   0.000
> CT2   CT   CT2  5 113.60   488.27   0.25619338.688
> HA   CT2CT  5 110.10   279.74   0.2179   18853.104
> CC   CT2CT  5 108.00   435.14   0.   0.000
> CT2   CT   OH1  5 110.10   633.46   0.   0.000
> OH1   CTCC  5 110.10   633.46   0.   0.000
> CT   OH1 H  5 106.00   481.16   0.   0.000
>
> [ dihedraltypes ]
> HA   CT2CC   OC  9   180.00   0.2092 6
> CT   CT2CC   OC  9   180.00   0.2092 6
> CT2   CT   CT2   CC  9 0.00   4. 3
> OH1   CT   CT2   CC  9 0.00   0.8368 3
> OH1   CT   CT2   HA  9 0.00   0.8368 3
> CCCT   CT2   CC  9 0.00   0.8368 3
> CCCT   CT2   HA  9 0.00   0.8368 3
> CT2   CT   CT2   HA  9 0.00   0.8368 3
> OH1   CTCC   OC  9 0.00   1.2000 2
> CT2   CTCC   OC  9   180.00   0.2092 6
> CCCT   OH1H  9 0.00   0.2092 1
> CT2   CT   OH1H  9 0.00   0.5858 3
> CC   CT2OC   OC  2 0.00  803.328
> CCCTOC   OC  2 0.00  803.328
>
> [ moleculetype ]
> CIT 3
>
> [ atoms ]
> 1   CC   1  CIT   C  1   0.62012.011
> 2   CT2  1  CIT   C  2  -0.18012.011
> 3   CT   1  CIT   C  3  -0.07012.011
> 4   CC   1  CIT   C  4   0.62012.011
> 5   CT2  1  CIT   C  5  -0.18012.011
> 6   CC   1  CIT   C  6   0.62012.011
> 7   OC   1  CIT   O  7  -0.76015.999
> 8   OC   1  CIT   O  8  -0.76015.999
> 9   OC   1  CIT   O  9  -0.76015.999
> 10  OC   1  CIT   O 10  -0.76015.999
> 11  OC   1  CIT   O 11  -0.76015.999
> 12  OC   1  CIT   O 12  -0.76015.999
> 13  OH1  1  CIT   O 13  -0.54015.999
> 14  HA   1  CIT   H 14   0.090 1.008
> 15  HA   1  CIT   H 15   0.090 1.008
> 16  HA   1  CIT   H 16   0.090 1.008
> 17  HA   1  CIT   H 17   0.090 1.008
> 18  H1  CIT   H 18   0.310 1.008
>
> [ bonds ]
> 1 81
> 1 71
> 1 2   1
> 2 15   1
> 2 14   1
> 2 31
> 3 13   1
> 3 51
> 3 41
> 4 10   1
> 4 91
> 5 17   1
> 5 16   1
> 5 61
> 6 12   1
> 6 11   1
> 13 18  1
> [ angles ]
> 8 1 7   5
> 8 1 2   5
> 7 1 2   5
> 1 215   5
> 15214   5
> 152 3   5
> 1 214   5
> 142 3   5
> 1 2 3   5
> 2 313   5
> 133 5   5
> 133 4   5
> 2 3 5   5
> 5 3 4   5
> 2 3 4   5
> 3 410   5
> 104 9   5
> 3 4 9   5
> 3 517   5
> 17516   5
> 175 6   5
> 3 516   5
> 165 6   5
> 3 5 6   5
> 5 612   5
> 12611   5
> 5 611   5
> 31318   5
>
> [ exclusions ]
> 18  9 10
>
> [ pairs ]
> 10 18 2 0.3 -0.760 0.310 0.17145 0.310857
> 9  18 2 0.3 -0.760 0.310 0.17145 0.310857
>
> [ dihedrals ]
> 812   15  9
> 712   15  9
> 812   14  9
> 712   14  9
> 8123  9
> 7123  9
> 123   13  9
> 15   23   13  9
> 14   23   13  9
> 1235  9
> 15   235  9
> 14   235  9
> 1234  9
> 15   234  9
> 14   234  9
> 23   13   18  9
> 53   13   18  9
> 43   13   18  9
> 235   17  9
> 13   35   17  9
> 435   17  9
> 235   16  9
> 13   35   16  9
> 435   16  9
> 2356  9
> 13   356  9
> 4356  9
> 234   10  9
> 13   34   10  9
> 534   10  9
> 2349  9
> 13   349  9
> 5349  9
> 356   12  9
> 17   56   12  9
> 16   56   12  9
> 356   11  9
> 17   56

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash

Sorry but I don't quite understand where the duplicates come from? I've pasted 
my itp file below: 

[ defaults ]
1 2 yes 1.0 1.0

[ atomtypes ]
OC  8 15. -0.760 A 0.302906 0.50208
CC  6 12.0110  0.620 A 0.356359 0.29288
HA  1  1.0080  0.090 A 0.235197 0.09205
CT2 6 12.0110 -0.180 A 0.387541 0.23012
CT  6 12.0110 -0.070 A 0.405359 0.08368
OH1 8 15. -0.540 A 0.315378 0.63639
H   1  1.0080  0.310 A 0.040001 0.19623

[ bondtypes ]
CC OC  1  0.126 439320.0
CC CT2 1  0.152 167360.0
CT2HA  1  0.111 258571.2
OH1H   1  0.096 456056.0
CT CC  1  0.152 167360.0
CT2CT  1  0.150 186188.0
CT OH1 1  0.142 358150.4

[ angletypes ]
OCCCOC  5 124.00   836.80   0.2225   58576.000
OCCC   CT2  5 118.00   334.72   0.2388   41840.000
CC   CT2HA  5 109.50   276.14   0.2163   25104.000
HA   CT2HA  5 109.00   297.06   0.18024518.720
CTCCOC  5 118.00   334.72   0.2388   41840.000
CT2   CTCC  5 108.00   435.14   0.   0.000
CT2   CT   CT2  5 113.60   488.27   0.25619338.688
HA   CT2CT  5 110.10   279.74   0.2179   18853.104
CC   CT2CT  5 108.00   435.14   0.   0.000
CT2   CT   OH1  5 110.10   633.46   0.   0.000
OH1   CTCC  5 110.10   633.46   0.   0.000
CT   OH1 H  5 106.00   481.16   0.   0.000

[ dihedraltypes ]
HA   CT2CC   OC  9   180.00   0.2092 6
CT   CT2CC   OC  9   180.00   0.2092 6
CT2   CT   CT2   CC  9 0.00   4. 3
OH1   CT   CT2   CC  9 0.00   0.8368 3
OH1   CT   CT2   HA  9 0.00   0.8368 3
CCCT   CT2   CC  9 0.00   0.8368 3
CCCT   CT2   HA  9 0.00   0.8368 3
CT2   CT   CT2   HA  9 0.00   0.8368 3
OH1   CTCC   OC  9 0.00   1.2000 2
CT2   CTCC   OC  9   180.00   0.2092 6
CCCT   OH1H  9 0.00   0.2092 1
CT2   CT   OH1H  9 0.00   0.5858 3
CC   CT2OC   OC  2 0.00  803.328
CCCTOC   OC  2 0.00  803.328

[ moleculetype ]
CIT 3

[ atoms ]
1   CC   1  CIT   C  1   0.62012.011
2   CT2  1  CIT   C  2  -0.18012.011
3   CT   1  CIT   C  3  -0.07012.011
4   CC   1  CIT   C  4   0.62012.011
5   CT2  1  CIT   C  5  -0.18012.011
6   CC   1  CIT   C  6   0.62012.011
7   OC   1  CIT   O  7  -0.76015.999
8   OC   1  CIT   O  8  -0.76015.999
9   OC   1  CIT   O  9  -0.76015.999
10  OC   1  CIT   O 10  -0.76015.999
11  OC   1  CIT   O 11  -0.76015.999
12  OC   1  CIT   O 12  -0.76015.999
13  OH1  1  CIT   O 13  -0.54015.999
14  HA   1  CIT   H 14   0.090 1.008
15  HA   1  CIT   H 15   0.090 1.008
16  HA   1  CIT   H 16   0.090 1.008
17  HA   1  CIT   H 17   0.090 1.008
18  H1  CIT   H 18   0.310 1.008

[ bonds ]
1 81
1 71
1 2   1
2 15   1
2 14   1
2 31
3 13   1
3 51
3 41
4 10   1
4 91
5 17   1
5 16   1
5 61
6 12   1
6 11   1
13 18  1
[ angles ]
8 1 7   5
8 1 2   5
7 1 2   5
1 215   5
15214   5
152 3   5
1 214   5
142 3   5
1 2 3   5
2 313   5
133 5   5
133 4   5
2 3 5   5
5 3 4   5
2 3 4   5
3 410   5
104 9   5
3 4 9   5
3 517   5
17516   5
175 6   5
3 516   5
165 6   5
3 5 6   5
5 612   5
12611   5
5 611   5
31318   5

[ exclusions ]
18  9 10

[ pairs ]
10 18 2 0.3 -0.760 0.310 0.17145 0.310857
9  18 2 0.3 -0.760 0.310 0.17145 0.310857

[ dihedrals ]
812   15  9
712   15  9
812   14  9
712   14  9
8123  9
7123  9
123   13  9
15   23   13  9
14   23   13  9
1235  9
15   235  9
14   235  9
1234  9
15   234  9
14   234  9
23   13   18  9
53   13   18  9
43   13   18  9
235   17  9
13   35   17  9
435   17  9
235   16  9
13   35   16  9
435   16  9
2356  9
13   356  9
4356  9
234   10  9
13   34   10  9
534   10  9
2349  9
13   349  9
5349  9
356   12  9
17   56   12  9
16   56   12  9
356   11  9
17   56   11  9
16   56   11  9

[ dihedrals ]
1  2  7 8 2
4  3  9 102
6  5  11122

#ifdef POSRES_CITMolecule 
[ position_restraints ] 
; atom  type  fx  fy  fz 
   1 1 1000 1000 1000 
   2 1 1000 1000 1000 
   3 1 1000 1000 1000 
   4 1 1000 1000 1000 
   5 1 1000 1000 1000 
   6 1 1000 1000 1000 
   7 1 1000 1000 1000 
   8 1 1000 1000 1000 
   9 1 1000 1000 1000 
  10 1 1000 1000 1000 
  11 1 1000 1000 1000 
  12 1 1000 1000 1000 
  13 1 1000 1000 1000
  14 1 1000 1000 1000
  15 1 1000 1000 1000
  16 1 1000 1000 1000
  17 1 1000 1000 1000  
  18 1 1000 1000 1000
#endif

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Justin Lemkul





On 4/12/19 10:52 AM, Pandya, Akash wrote:

Hi all,

My simulation contains citrate molecules. When I try to solvate the system, I 
get this error. Can anybody help with this?


Your citrate topology is introducing duplicate parameters that already 
exist in the force field. In this instance, they appear to be exact 
copies (at least for the bonded parameters shown) but this is bad 
practice. Eliminate the redundancies.


-Justin


WARNING 1 [file CITff.itp, line 3]:
   Overriding atomtype OC


WARNING 2 [file CITff.itp, line 4]:
   Overriding atomtype CC


WARNING 3 [file CITff.itp, line 5]:
   Overriding atomtype HA


WARNING 4 [file CITff.itp, line 6]:
   Overriding atomtype CT2


WARNING 5 [file CITff.itp, line 7]:
   Overriding atomtype CT


WARNING 6 [file CITff.itp, line 8]:
   Overriding atomtype OH1


WARNING 7 [file CITff.itp, line 9]:
   Overriding atomtype H


WARNING 8 [file CITff.itp, line 13]:
   Overriding Bond parameters.

   old:  0.1522 167360 0.1522 167360
   new: CC CT2 1  0.152 167360.0


WARNING 9 [file CITff.itp, line 14]:
   Overriding Bond parameters.

   old:  0. 258571 0. 258571
   new: CT2HA  1  0.111 258571.2


WARNING 10 [file CITff.itp, line 23]:
   Overriding U-B parameters.

   old:  109.5 276.144 0.2163 25104 
109.5 276.144 0.2163 25104
   new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000


WARNING 11 [file CITff.itp, line 24]:
   Overriding U-B parameters.

   old:  109 297.064 0.1802 4518.72 109 
297.064 0.1802 4518.72
   new: HA   CT2HA  5 109.00   297.06   0.18024518.720

Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_H'
Excluding 3 bonded neighbours molecule type 'CIT'
Excluding 3 bonded neighbours molecule type 'GLY'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 62703]:
   System has non-zero total charge: -46.95
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.



Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  1366Protein residues
There are:23  Other residues
There are: 56714  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...
Number of degrees of freedom in T-Coupling group rest is 389088.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 104x104x104, spacing 0.120 0.120 0.120
Estimate for the relative computational load of the PME mesh part: 0.19
This run will generate roughly 14 Mb of data

There were 2 notes

There were 11 warnings

---
Program: gmx grompp, version 2016.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)

Fatal error:
Too many warnings (11).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash

I'm using the CHARMM27 FF and I obtained the parameters from literature.

Akash 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Soham Sarkar
Sent: 12 April 2019 16:05
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters

Which force field you are using and how you made the itp of the citrate 
molecule?

On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash, 
wrote:

> Hi all,
>
> My simulation contains citrate molecules. When I try to solvate the 
> system, I get this error. Can anybody help with this?
>
> WARNING 1 [file CITff.itp, line 3]:
>   Overriding atomtype OC
>
>
> WARNING 2 [file CITff.itp, line 4]:
>   Overriding atomtype CC
>
>
> WARNING 3 [file CITff.itp, line 5]:
>   Overriding atomtype HA
>
>
> WARNING 4 [file CITff.itp, line 6]:
>   Overriding atomtype CT2
>
>
> WARNING 5 [file CITff.itp, line 7]:
>   Overriding atomtype CT
>
>
> WARNING 6 [file CITff.itp, line 8]:
>   Overriding atomtype OH1
>
>
> WARNING 7 [file CITff.itp, line 9]:
>   Overriding atomtype H
>
>
> WARNING 8 [file CITff.itp, line 13]:
>   Overriding Bond parameters.
>
>   old:  0.1522 167360 0.1522 167360
>   new: CC CT2 1  0.152 167360.0
>
>
> WARNING 9 [file CITff.itp, line 14]:
>   Overriding Bond parameters.
>
>   old:  0. 258571 0. 258571
>   new: CT2HA  1  0.111 258571.2
>
>
> WARNING 10 [file CITff.itp, line 23]:
>   Overriding U-B parameters.
>
>   old:  109.5 276.144 0.2163 25104
> 109.5 276.144 0.2163 25104
>   new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000
>
>
> WARNING 11 [file CITff.itp, line 24]:
>   Overriding U-B parameters.
>
>   old:  109 297.064 0.1802 4518.72
> 109 297.064 0.1802 4518.72
>   new: HA   CT2HA  5 109.00   297.06   0.18024518.720
>
> Generated 20503 of the 20503 non-bonded parameter combinations 
> Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 
> 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 
> 'Protein_chain_H'
> Excluding 3 bonded neighbours molecule type 'CIT'
> Excluding 3 bonded neighbours molecule type 'GLY'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 62703]:
>   System has non-zero total charge: -46.95
>   Total charge should normally be an integer. See
>   
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FFloating_Point_Arithmeticdata=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906783645721595sdata=mMSRKLOaTcASmbpt%2BVctQztiZY%2F6xpgswsGtQUIrI5s%3Dreserved=0
>   for discussion on how close it should be to an integer.
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet Analysing 
> residue names:
> There are:  1366Protein residues
> There are:23  Other residues
> There are: 56714  Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and 
> splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 389088.00 
> Calculating fourier grid dimensions for X Y Z Using a fourier grid of 
> 104x104x104, spacing 0.120 0.120 0.120 Estimate for the relative 
> computational load of the PME mesh part: 0.19 This run will generate 
> roughly 14 Mb of data
>
> There were 2 notes
>
> There were 11 warnings
>
> ---
> Program: gmx grompp, version 2016.2
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)
>
> Fatal error:
> Too many warnings (11).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the 
> GROMACS website at 
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g
> romacs.org%2FDocumentation%2FErrorsdata=02%7C01%7Cakash.pandya.15
> %40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c9
> 210a11d9a5c2%7C0%7C0%7C636906783645721595sdata=dF0uRrtoKsq3K9uJyL
> w60UZo3bwuWC4%2BYlMGrBRzaDA%3Dreserved=0
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g
> romacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906783645721595sdata=HyijvyY8LCx2ejwkReuWkGjI2MF%2FtSWqLli7OhFiWjM%3Dreserved=0
>  before posting!
>
> * Can't post? Read 
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> 5%40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c
> 9210a11d9a5c2%7C0%7C0%7C636906783645721595sdata=IIXN2GwxJNCG5DhdK
>

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Soham Sarkar

Which force field you are using and how you made the itp of the citrate
molecule?

On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash, 
wrote:

> Hi all,
>
> My simulation contains citrate molecules. When I try to solvate the
> system, I get this error. Can anybody help with this?
>
> WARNING 1 [file CITff.itp, line 3]:
>   Overriding atomtype OC
>
>
> WARNING 2 [file CITff.itp, line 4]:
>   Overriding atomtype CC
>
>
> WARNING 3 [file CITff.itp, line 5]:
>   Overriding atomtype HA
>
>
> WARNING 4 [file CITff.itp, line 6]:
>   Overriding atomtype CT2
>
>
> WARNING 5 [file CITff.itp, line 7]:
>   Overriding atomtype CT
>
>
> WARNING 6 [file CITff.itp, line 8]:
>   Overriding atomtype OH1
>
>
> WARNING 7 [file CITff.itp, line 9]:
>   Overriding atomtype H
>
>
> WARNING 8 [file CITff.itp, line 13]:
>   Overriding Bond parameters.
>
>   old:  0.1522 167360 0.1522 167360
>   new: CC CT2 1  0.152 167360.0
>
>
> WARNING 9 [file CITff.itp, line 14]:
>   Overriding Bond parameters.
>
>   old:  0. 258571 0. 258571
>   new: CT2HA  1  0.111 258571.2
>
>
> WARNING 10 [file CITff.itp, line 23]:
>   Overriding U-B parameters.
>
>   old:  109.5 276.144 0.2163 25104
> 109.5 276.144 0.2163 25104
>   new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000
>
>
> WARNING 11 [file CITff.itp, line 24]:
>   Overriding U-B parameters.
>
>   old:  109 297.064 0.1802 4518.72
> 109 297.064 0.1802 4518.72
>   new: HA   CT2HA  5 109.00   297.06   0.18024518.720
>
> Generated 20503 of the 20503 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17396 of the 20503 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_H'
> Excluding 3 bonded neighbours molecule type 'CIT'
> Excluding 3 bonded neighbours molecule type 'GLY'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 62703]:
>   System has non-zero total charge: -46.95
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:  1366Protein residues
> There are:23  Other residues
> There are: 56714  Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 389088.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 104x104x104, spacing 0.120 0.120 0.120
> Estimate for the relative computational load of the PME mesh part: 0.19
> This run will generate roughly 14 Mb of data
>
> There were 2 notes
>
> There were 11 warnings
>
> ---
> Program: gmx grompp, version 2016.2
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)
>
> Fatal error:
> Too many warnings (11).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash

Hi all,

My simulation contains citrate molecules. When I try to solvate the system, I 
get this error. Can anybody help with this?

WARNING 1 [file CITff.itp, line 3]:
  Overriding atomtype OC


WARNING 2 [file CITff.itp, line 4]:
  Overriding atomtype CC


WARNING 3 [file CITff.itp, line 5]:
  Overriding atomtype HA


WARNING 4 [file CITff.itp, line 6]:
  Overriding atomtype CT2


WARNING 5 [file CITff.itp, line 7]:
  Overriding atomtype CT


WARNING 6 [file CITff.itp, line 8]:
  Overriding atomtype OH1


WARNING 7 [file CITff.itp, line 9]:
  Overriding atomtype H


WARNING 8 [file CITff.itp, line 13]:
  Overriding Bond parameters.

  old:  0.1522 167360 0.1522 167360
  new: CC CT2 1  0.152 167360.0


WARNING 9 [file CITff.itp, line 14]:
  Overriding Bond parameters.

  old:  0. 258571 0. 258571
  new: CT2HA  1  0.111 258571.2


WARNING 10 [file CITff.itp, line 23]:
  Overriding U-B parameters.

  old:  109.5 276.144 0.2163 25104 
109.5 276.144 0.2163 25104
  new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000


WARNING 11 [file CITff.itp, line 24]:
  Overriding U-B parameters.

  old:  109 297.064 0.1802 4518.72 109 
297.064 0.1802 4518.72
  new: HA   CT2HA  5 109.00   297.06   0.18024518.720

Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_H'
Excluding 3 bonded neighbours molecule type 'CIT'
Excluding 3 bonded neighbours molecule type 'GLY'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 62703]:
  System has non-zero total charge: -46.95
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  1366Protein residues
There are:23  Other residues
There are: 56714  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...
Number of degrees of freedom in T-Coupling group rest is 389088.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 104x104x104, spacing 0.120 0.120 0.120
Estimate for the relative computational load of the PME mesh part: 0.19
This run will generate roughly 14 Mb of data

There were 2 notes

There were 11 warnings

---
Program: gmx grompp, version 2016.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)

Fatal error:
Too many warnings (11).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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Re: [gmx-users] Energy from a subgroup of molecules

2019-04-12 Thread paul buscemi

Thank you Justin.  

Using energy groups is not really that bad.  

By using  gmx select ‘atomname Cx and resname ADSORBATE and within 0.5 of 
resname SURFACE’ -on near.ndx

I can find  the atom/s of the adsorbate that is proximal to the surface and  
can track the LJ pot’l by frame and use VMD for further analysis

Paul

> On Apr 11, 2019, at 5:57 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 4/11/19 5:39 PM, paul buscemi wrote:
>> Thank you for the response, Mark.
>> 
>> I do use the rerun tactic, and this is not too bad for a small number of 
>> molecules
>> 
>>  but is there a way to include the index information within the mdrun (rerun 
>> ) … something like
>> 
>> gmx mdrun  -s adsorb.ener_gp.tpr  -rerun adsorb,npt.trr   - n use_only.ndx  ?
>> 
>> or use the  indices within the grompp command ?
>> 
> 
> The only solution is what Mark proposed - create a .tpr file with the 
> required energygrps and use mdrun -rerun. mdrun does not accept an index file.
> 
> -Justin
> 
>> Paul
>> 
>>> On Apr 11, 2019, at 1:48 AM, Mark Abraham  wrote:
>>> 
>>> Hi,
>>> 
>>> You can't do that with gmx energy, as you need mdrun to understand the new
>>> grouping. But making a new .tpr with the energy groups so defined permits
>>> you to use gmx mdrun -rerun for such a single point energy evaluation.
>>> 
>>> Mark
>>> 
>>> On Wed., 10 Apr. 2019, 22:24 p buscemi,  wrote:
>>> 
 Dear Users,
 I've performed an adsorption experiment in which a fraction of molecules
 in solution adsorb to a surface. I can extract the index of those adsorbed,
 and I can obtain the total interaction ( LJ ) of the energy group with the
 surface.
 I can estimate the average interaction of the adsorbed molecules by
 dividing the total energy by the number of molecules within a certain
 distance ( the index number )
 How might I use gmx energy to recalculate the interaction using the
 original surface but only the adsorbed molecules specified in the index
 file... something like
 "gmx energy -f starting.gro -n index.ndx"
 
 A single point calculation would be quite satisfactory.
 thanks
 Paul
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> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> 
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
> 
> ==
> 
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Re: [gmx-users] Tpr version check

2019-04-12 Thread Erik Marklund

Hi,

Thanks Mark. See https://redmine.gromacs.org/issues/2924.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se

On 11 Apr 2019, at 08:42, Mark Abraham 
mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

The old behavior of a graceful rejection of the file with a new version
number is still expected.

The most likely explanation for your observations is that they old version
of gmx is linking somehow to newer versions of things (which also shouldn't
happen ...), and the chimera can't work.
If you can share a tpr on Redmine we can see if there is an issue we can
fix.

Mark

On Wed., 10 Apr. 2019, 23:05 Erik Marklund, 
mailto:erik.markl...@kemi.uu.se>>
wrote:

Hi users,

I accidentally used an older version (2016.3) to run trjconv on some
trajectories. Some conversions worked, seemingly depending on pbc options
etc, whereas others stopped with the following output:

Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
->  frame  0 time0.000
---
Program: gmx trjconv, version 2016.3
Source file: src/gromacs/pbcutil/pbc.cpp (line 94)

Fatal error:
Unknown ePBC=1051770189 in ePBC2npbcdim

Call me a hopeless nostalgic, but I remember a time when such mistakes
rendered an error saying that I am using an older version of gmx than the
version used to generate the tpr file. Is that not a thing anymore, and
this is the expected behaviour? Seems problematic if gmx tools try to read
nonsense data (from the viewpoint of the gromacs version used).

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se









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Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

Re: [gmx-users] Citrate parameters

[gmx-users] Citrate parameters

Re: [gmx-users] Energy from a subgroup of molecules

Re: [gmx-users] Tpr version check

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